Help Regarding GCRMA Human Exon.
125 views
Skip to first unread message
Prithish Banerjee
Dec 2, 2010, 3:08:41 PM12/2/10
to aroma-af...@googlegroups.com
Respected Dr Bengtsson,
I have the following codes and outputs:
> source("http://aroma-project.org/hbLite.R");
> hbInstall("aroma.affymetrix")
> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
> dataSet <- "Exon Data"
> chipType <- "HuEx-1_0-st-v2"
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuEx-1_0-st-v2
Filename: HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf
Filesize: 203.31MB
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 297051
Cells per unit: 22.06
Number of QC units: 1
> ptf <- AffymetrixProbeTabFile$byChipType(chipType);
> print(ptf)
AffymetrixProbeTabFile:
Name: HuEx-1_0-st-v2
Tags:
Full name: HuEx-1_0-st-v2
Pathname: annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
File size: 527.80 MB (553438704 bytes)
RAM: 0.01 MB
Number of data rows: NA
Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos', 'assembly', 'seqname', 'start', 'stop', 'strand', 'probeSequence', 'targetStrandedness', 'category'
Number of text lines: NA
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuEx-1_0-st-v2
Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
Filesize: 38.25MB
Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 18708
Cells per unit: 350.31
Number of QC units: 1
> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType,cdf=cdf)
> print(csR)
AffymetrixCelSet:
Name: Exon Data
Tags:
Path: rawData/Exon Data/HuEx-1_0-st-v2
Platform: Affymetrix
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
Number of arrays: 17
Names: 10_5N, 11_6T, ..., 9_5T
Time period: 2005-05-25 15:34:12 -- 2005-05-26 07:49:40
Total file size: 1081.22MB
RAM: 0.02MB
> bc <- GcRmaBackgroundCorrection(csR, type="affinities")
> print(bc)
GcRmaBackgroundCorrection:
Data set: Exon Data
Input tags:
User tags: *
Asterisk ('*') tags: GRBC
Output tags: GRBC
Number of files: 17 (1081.22MB)
Platform: Affymetrix
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm", indicesNegativeControl: NULL, affinities: NULL, type: chr "affinities", opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
Output path: probeData/Exon Data,GRBC/HuEx-1_0-st-v2
Is done: FALSE
RAM: 0.00MB
> csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose)
20101202 14:46:02|Background correcting data set...
20101202 14:46:02| Computing probe affinities (independent of data)...
20101202 14:46:03| Computing GCRMA probe affinities...
20101202 14:46:03| Chip type: HuEx-1_0-st-v2
20101202 14:46:03| Number of units: 297051
20101202 14:46:03| Locating the cell sequence annotation data file...
20101202 14:46:03| Locating the cell sequence annotation data file...done
20101202 14:46:03| Computing GCRMA probe affinities...done
20101202 14:46:03| Computing GCRMA probe affinities...
20101202 14:46:03| Number of units: 297051
20101202 14:46:03| Identify PMs and MMs among the CDF cell indices...
logi [1:5270074] TRUE TRUE TRUE TRUE TRUE TRUE ...
Mode TRUE NA's
logical 5270074 0
20101202 14:46:52| MMs are defined as non-PMs
20101202 14:46:52| Number of PMs: 5270074
20101202 14:46:52| Number of MMs: 0
20101202 14:46:52| Identify PMs and MMs among the CDF cell indices...done
20101202 14:46:52| Reading probe-sequence data...
20101202 14:46:52| Retrieving probe-sequence data...
20101202 14:46:52| Chip type (full): HuEx-1_0-st-v2,fullR3,A20071112,EP
20101202 14:46:52| Locating probe-tab file...
20101202 14:46:52| Chip type: HuEx-1_0-st-v2
AffymetrixProbeTabFile:
Name: HuEx-1_0-st-v2
Tags:
Full name: HuEx-1_0-st-v2
Pathname: annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
File size: 527.80 MB (553438704 bytes)
RAM: 0.01 MB
Number of data rows: NA
Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos', 'assembly', 'seqname', 'start', 'stop', 'strand', 'probeSequence', 'targetStrandedness', 'category'
Number of text lines: NA
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuEx-1_0-st-v2
Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
Filesize: 38.25MB
Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 18708
Cells per unit: 350.31
Number of QC units: 1
20101202 14:46:52| Locating probe-tab file...done
20101202 14:46:52| Validating probe-tab file against CDF...
20101202 14:46:52| Number of records read: 1
20101202 14:46:52| Data read:
'data.frame': 1 obs. of 1 variable:
$ probeSetID: chr "2315101"
- attr(*, "fileHeader")=List of 6
..$ comments: NULL
..$ sep : chr "\t"
..$ quote : chr "\""
..$ skip : num 0
..$ topRows :List of 10
.. ..$ : chr "Probe ID" "Probe Set ID" "probe x" "probe y" ...
.. ..$ : chr "494998" "2315101" "917" "193" ...
.. ..$ : chr "1734213" "2315101" "1092" "677" ...
.. ..$ : chr "4767517" "2315101" "796" "1862" ...
.. ..$ : chr "4286427" "2315101" "986" "1674" ...
.. ..$ : chr "5760145" "2315102" "144" "2250" ...
.. ..$ : chr "671410" "2315102" "689" "262" ...
.. ..$ : chr "4275780" "2315102" "579" "1670" ...
.. ..$ : chr "4293462" "2315102" "341" "1677" ...
.. ..$ : chr "5388" "2315103" "267" "2" ...
..$ columns : chr "Probe ID" "Probe Set ID" "probe x" "probe y" ...
20101202 14:46:52| Unit name:
chr "2315101"
20101202 14:46:55| Unit index: NA
Error in list(`process(bc, cdf = cdf, ptf = ptf, verbose = verbose)` = <environment>, :
[2010-12-02 14:46:55] Exception: Failed to identify CDF unit with unit name '2315101': annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
at throw(Exception(...))
at throw.default("Failed to identify CDF unit with unit name '", unitNa
at throw("Failed to identify CDF unit with unit name '", unitName, "':
at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
at getProbeSequenceData(this, safe = safe, verbose = verbose)
at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver
at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos
at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon Data,GRBC/
at bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/HuEx-1_0-st-v2",
at do.call("bgAdjustGcrma", args = args)
at process.GcRmaBackgroundCorrection(bc, cdf = cdf, ptf = ptf, verbose
at process(bc, cdf = cdf, ptf = ptf, verbose = verbose)
20101202 14:46:55| Validating probe-tab file against CDF...done
20101202 14:46:55| Retrieving probe-sequence data...done
20101202 14:46:55| Reading probe-sequence data...done
20101202 14:46:55| Computing GCRMA probe affinities...done
20101202 14:46:55| Computing probe affinities (independent of data)...done
20101202 14:46:55|Background correcting data set...done
Could you please tell me how to rectify the error?
Thank you.
Prithish Banerjee,
Graduate Research Assistant,
Department of Statistics,
West Virginia University.
Graduate Research Assistant,
Department of Statistics,
West Virginia University.
Henrik Bengtsson
Dec 3, 2010, 2:50:07 AM12/3/10
to aroma-affymetrix
Hi.
On Thu, Dec 2, 2010 at 12:08 PM, Prithish Banerjee
<prithish...@gmail.com> wrote:
> Respected Dr Bengtsson,
> I have the following codes and outputs:
>> source("http://aroma-project.org/hbLite.R");
>> hbInstall("aroma.affymetrix")
I'll assume that you've run this recently so that you have
aroma.affymetrix v1.8.0 installed, because then you can do what I
explain next. FYI, whenever you get an error, please report what
sessionInfo() gives so we can be sure you're up-to-date.
Go to the HuEx-1_0-st-v2 chip type page:
http://aroma-project.org/chipTypes/HuEx-1_0-st-v2/
and download the Aroma Cell Sequence (ACS) file. Place it in
annotationData/chipTypes/HuEx-1_0-st-v2/ (where your CDF is). Don't
forget to gunzip.
You can drop/move/leave the probe-tab file; it won't be needed anymore.
The following script should do:
verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
dataSet <- "Exon Data";
chipType <- "HuEx-1_0-st-v2";
cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP");
print(cdf);
# Assert that the ACS file is available (not really needed to be done)
acs <- getAromaCellSequenceFile(cdf);
print(acs);
# GCRMA background correction
bc <- GcRmaBackgroundCorrection(csR, type="affinities");
print(bc);
csB <- process(bc, verbose=verbose);
print(csB);
Finally, I've noticed that you've tried to pass arguments 'cdf' and
'ptf' to process(), i.e.
csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose);
That is not correct. Was that suggested to you anywhere, or is it
just part of your trial-and-error?
Let me know if this solves your problem
/Henrik
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-af...@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
Yan Jiao
Dec 3, 2010, 10:59:00 AM12/3/10
to aroma-af...@googlegroups.com
Hi,
First of all, I have to say I've got tremendous help from this mailing list, thank you for all of you.
Then I have to continue asking for help,
I just realize I probably did something very stupid,
I was doing DNA copy number segmentation, affymetrix 100k SNP, so as far as I know there are two chips, one chip is obtained by digesting the DNA with Hind, the other chip by Xba.Chip, so in my rawdata folder , I got the .CEL file from both, but in the annotationData folder, sub folder :type, I only got Mapping50K_Hind240,and .cdf file, .ufl, ugp file for hind.
My question is, Should I firstly split the .cel file accoding to the chip type and then found the corresponding cdf file etc for Xba.
Many thanks
Yan
**********************************************************************
This email and any files transmitted with it are confidential and
intended solely for the use of the individual or entity to whom they
are addressed. If you have received this email in error please notify
the system manager (it.su...@cancer.ucl.ac.uk).
**********************************************************************
First of all, I have to say I've got tremendous help from this mailing list, thank you for all of you.
Then I have to continue asking for help,
I just realize I probably did something very stupid,
I was doing DNA copy number segmentation, affymetrix 100k SNP, so as far as I know there are two chips, one chip is obtained by digesting the DNA with Hind, the other chip by Xba.Chip, so in my rawdata folder , I got the .CEL file from both, but in the annotationData folder, sub folder :type, I only got Mapping50K_Hind240,and .cdf file, .ufl, ugp file for hind.
My question is, Should I firstly split the .cel file accoding to the chip type and then found the corresponding cdf file etc for Xba.
Many thanks
Yan
This email and any files transmitted with it are confidential and
intended solely for the use of the individual or entity to whom they
are addressed. If you have received this email in error please notify
the system manager (it.su...@cancer.ucl.ac.uk).
**********************************************************************
Prithish Banerjee
Dec 3, 2010, 2:22:47 PM12/3/10
to aroma-af...@googlegroups.com
Respected Dr Bengtsson,
Prithish Banerjee,
Graduate Research Assistant,
Department of Statistics,
Thank you for your help. Sorry for not providing the sessionInfo() last time. I am using aroma.affymetrix v 1.8.0. It solved that error but I am facing a new error this time. The sessionInfo and the outputs are as follows:
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.affymetrix_1.8.0 aroma.apd_0.1.7 affxparser_1.22.0
[4] R.huge_0.2.0 aroma.core_1.8.0 aroma.light_1.18.2
[7] matrixStats_0.2.2 R.rsp_0.4.0 R.filesets_0.9.1
[10] digest_0.4.2 R.cache_0.3.0 R.utils_1.5.8
[13] R.oo_1.7.4 R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] affy_1.28.0 affyio_1.18.0 Biobase_2.10.0
[4] Biostrings_2.18.0 gcrma_2.22.0 IRanges_1.8.2
[7] preprocessCore_1.12.0 splines_2.12.0 tools_2.12.0
> source("http://aroma-project.org/hbLite.R");
> hbInstall("aroma.affymetrix")
> source("http://aroma-project.org/hbLite.R");
> hbInstall("aroma.cn")
> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
> dataSet <- "Exon Data"
> chipType <- "HuEx-1_0-st-v2"
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP")
> print(cdf)
> acs<-getAromaCellSequenceFile(cdf)
> print(acs)
> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType,cdf=cdf)
> bc <- GcRmaBackgroundCorrection(csR, type="affinities")
> print(bc)
GcRmaBackgroundCorrection:
Data set: Exon Data
Input tags:
User tags: *
Asterisk ('*') tags: GRBC
Output tags: GRBC
Number of files: 4 (251.42MB)
Platform: Affymetrix
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm", indicesNegativeControl: NULL, affinities: NULL, type: chr "affinities", opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
Output path: probeData/Exon Data,GRBC/HuEx-1_0-st-v2
Is done: FALSE
RAM: 0.00MB
> csB <- process(bc, verbose=verbose)
20101203 14:04:42|Background correcting data set...
20101203 14:04:42| Computing probe affinities (independent of data)...
20101203 14:04:42| Computing GCRMA probe affinities...
20101203 14:04:42| Chip type: HuEx-1_0-st-v2
20101203 14:04:42| Number of units: 297051
20101203 14:04:43| Cached results found.
20101203 14:04:43| Computing GCRMA probe affinities...done
20101203 14:04:43| RAM: 50.00MB
20101203 14:04:43| Computing probe affinities (independent of data)...done
20101203 14:04:43| Background correcting data set...
20101203 14:04:44| Already background corrected for "optical" effects
20101203 14:04:44| Background correcting data set...done
20101203 14:04:44| Estimating specific binding parameters (data dependent)...
20101203 14:04:44| Extracting PM indices...
20101203 14:04:44| Reading cell indices from CDF file...
20101203 14:04:44| Pathname: annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf
20101203 14:04:44| Units:
NULL
20101203 14:04:44| lapplyInChunks()...
20101203 14:04:44| Number of elements per chunk: 1e+05
20101203 14:04:44| Chunk #1 of 3...
20101203 14:04:44| Elements:
int [1:100000] 1 2 3 4 5 6 7 8 9 10 ...
20101203 14:04:44| Querying CDF file...
20101203 14:05:08| Querying CDF file...done
20101203 14:05:08| Restructuring...
20101203 14:05:08| Restructuring...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 5354837 143.0 6193578 165.4 5373715 143.5
Vcells 13471411 102.8 20149605 153.8 13475095 102.9
20101203 14:05:09| Chunk #1 of 3...done
20101203 14:05:09| Chunk #2 of 3...
20101203 14:05:09| Elements:
int [1:100000] 100001 100002 100003 100004 100005 100006 100007 100008 100009 100010 ...
20101203 14:05:09| Querying CDF file...
20101203 14:05:15| Querying CDF file...done
20101203 14:05:15| Restructuring...
20101203 14:05:15| Restructuring...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1491395 39.9 4954862 132.4 6193578 165.4
Vcells 10685280 81.6 20149605 153.8 17357812 132.5
20101203 14:05:16| Chunk #2 of 3...done
20101203 14:05:16| Chunk #3 of 3...
20101203 14:05:16| Elements:
int [1:97051] 200001 200002 200003 200004 200005 200006 200007 200008 200009 200010 ...
20101203 14:05:16| Querying CDF file...
20101203 14:05:20| Querying CDF file...done
20101203 14:05:21| Restructuring...
20101203 14:05:21| Restructuring...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1471326 39.3 4954862 132.4 6193578 165.4
Vcells 10882001 83.1 20149605 153.8 17357812 132.5
20101203 14:05:21| Chunk #3 of 3...done
20101203 14:05:21| lapplyInChunks()...done
20101203 14:05:21| Reading cell indices from CDF file...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 336599 9.0 3963889 105.9 6193578 165.4
Vcells 9592574 73.2 20149605 153.8 17357812 132.5
20101203 14:05:21| readUnits.AffymetrixCdfFile(): Updating cache
20101203 14:05:49| Extracting PM indices...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 336674 9.0 2849399 76.1 6193578 165.4
Vcells 7232054 55.2 23577885 179.9 23043337 175.9
20101203 14:05:49| Extracting 25000 random PM intensities across CEL set...
20101203 14:05:49| Array #1 of 4...
20101203 14:05:50| Array #1 of 4...done
20101203 14:05:50| Array #2 of 4...
20101203 14:05:50| Array #2 of 4...done
20101203 14:05:50| Array #3 of 4...
20101203 14:05:50| Array #3 of 4...done
20101203 14:05:50| Array #4 of 4...
20101203 14:05:50| Array #4 of 4...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 337074 9.1 2279519 60.9 6193578 165.4
Vcells 7257179 55.4 23577885 179.9 23043337 175.9
20101203 14:05:50| Extracting 25000 random PM intensities across CEL set...done
20101203 14:05:50| Extracting probe affinities and fitting linear model...
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 337074 9.1 1823615 48.7 6193578 165.4
Vcells 7269671 55.5 23577885 179.9 23043337 175.9
20101203 14:05:51| Fitting the GCRMA background linear model...
num [1:25000] 6.13 10.17 5.73 7.87 10.87 ...
num [1:25000] 0.097 0.771 0.181 0.443 1.88 ...
Call:
lm(formula = pm.random2 ~ aff)
Coefficients:
(Intercept) aff
7.104 0.597
20101203 14:05:51| Fitting the GCRMA background linear model...done
20101203 14:05:51| Extracting probe affinities and fitting linear model...done
20101203 14:05:51| parametersGsb:
(Intercept) aff
7.1042892 0.5969684
20101203 14:05:51| Estimating specific binding parameters (data dependent)...done
20101203 14:05:51| Adjusting 4 arrays...
20101203 14:05:51| Array #1 of 4...
AffymetrixCelFile:
Name: 10 ZEB1_(HuEx-1_0-st-v2)
Tags:
Full name: 10 ZEB1_(HuEx-1_0-st-v2)
Pathname: probeData/Exon Data,OBC/HuEx-1_0-st-v2/10 ZEB1_(HuEx-1_0-st-v2).CEL
File size: 62.50 MB (65536714 bytes)
RAM: 0.00 MB
File format: v4 (binary; XDA)
Platform: Affymetrix
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
Timestamp: 2010-12-03 13:43:43
20101203 14:05:51| Retrieving PM and MM signals and affinities...
20101203 14:06:26| Number of PM probes: 5270074
20101203 14:06:26| Number of MM probes: 0
20101203 14:06:42| PM signals:
num [1:5270074] 237 480 120 482 421 ...
20101203 14:06:42| MM signals:
num(0)
20101203 14:06:43| PM affinities:
num [1:5270074] -0.585 -1.687 -1.664 -0.569 1.626 ...
20101203 14:06:43| MM affinities:
num(0)
20101203 14:06:43| Retrieving PM and MM signals and affinities...done
20101203 14:06:43| Estimating non-specific binding parameters...
20101203 14:06:43| Model type/flavor: affinities
20101203 14:06:43| Affinity-based GCRMA model background adjustment...
20101203 14:06:43| Using mismatch probes (MMs) as negative controls
20101203 14:06:43| Dropping perfect-match probes (PMs) with missing signals or missing affinities...
20101203 14:06:43| Number of finite PMs: 5270074 out of 5270074 (100.0%)
20101203 14:06:43| Number of finite PM affinities: 5270074 out of 5270074 (100.0%)
20101203 14:06:44| Number of PMs kept: 5270074 out of 5270074 (100.0%)
20101203 14:06:45| Dropping perfect-match probes (PMs) with missing signals or missing affinities...done
20101203 14:06:45| Dropping negative controls with missing signals or missing affinities...
20101203 14:06:45| Number of finite negative controls: 0 out of 0 (NaN%)
20101203 14:06:45| Number of finite negative-control affinities: 0 out of 0 (NaN%)
20101203 14:06:45| Number of negative controls kept: 0 out of 0 (NaN%)
20101203 14:06:45| Dropping negative controls with missing signals or missing affinities...done
20101203 14:06:45| Number of PMs: 5270074
20101203 14:06:45| Number of negative controls: 0
Error in if (from == to) rep.int(from, length.out) else as.vector(c(from, :
missing value where TRUE/FALSE needed
20101203 14:06:49| Array #1 of 4...done
20101203 14:06:49| Adjusting 4 arrays...done
20101203 14:06:49|Background correcting data set...done
Please help me in this regard. Also The passing of cdf and ptf arguments in process() is just the trial-error I was trying. I am really sorry for that and should have given you the code I have.
Yours Faithfully,
Graduate Research Assistant,
Department of Statistics,
West Virginia University.
Henrik Bengtsson
Dec 3, 2010, 8:45:26 PM12/3/10
to aroma-affymetrix
Hi,
sorry, it turns out that you also have to use the unsupported CDF for
the GCRMA step. It is only needed for that step, hence the setCdf():s
set & undo. You can download a binary version of HuEx-1_0-st-v2.cdf
at:
http://aroma-project.org/chipTypes/HuEx-1_0-st-v2
Then do:
library("aroma.affymetrix");
verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
dataSet <- "Exon Data";
chipType <- "HuEx-1_0-st-v2";
# The unsupported CDF
cdfS <- AffymetrixCdfFile$byChipType(chipType);
print(cdfS);
# The custom CDF
cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP");
print(cdf);
# Setup data set
csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf);
# GCRMA background correction
setCdf(csR, cdfS); # Set temporarily
bc <- GcRmaBackgroundCorrection(csR, type="affinities");
print(bc);
csB <- process(bc, verbose=verbose);
setCdf(csR, cdf); # Undo.
setCdf(csB, cdf); # Undo.
print(csB);
That should do it.
FYI, when doing AffymetrixCelSet$byName(...) specify either argument
'chipType' or 'cdf' - not both.
/Henrik
On Fri, Dec 3, 2010 at 11:22 AM, Prithish Banerjee
Prithish Banerjee
Dec 4, 2010, 5:43:58 PM12/4/10
to aroma-af...@googlegroups.com
Respected Dr Bengtsson,
Prithish Banerjee,
Graduate Research Assistant,
Department of Statistics,
Thank you very much for your help. It fixed the error and ran the GCRMA for human exon arrays. Thank you again for your help and support.
Yours Faithfully,
Graduate Research Assistant,
Department of Statistics,
West Virginia University.
Reply all
Reply to author
Forward
0 new messages