Error: object 'csC' not found.

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wxp...@gmail.com

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Jan 13, 2016, 1:02:09 PM1/13/16
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Hi dear professor   Henrik Bengtsson,

When I was declaring the raw data set of CytoScan HD Array with aroma.affymetrix, I'm encountering the following errors: 

"Error: object 'csC' not found." 

I have searched the forum, unfortunately, I can't solve this problem.

Could you give me some suggestions and help me solve it ?

The following are the R code of mine:

> setwd("G:/")

>library("aroma.affymetrix")

>log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)

>options(digits=4)

>cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array")

>gi <- getGenomeInformation(cdf)

>si <- getSnpInformation(cdf)

>acs <- AromaCellSequenceFile$byChipType(getChipType(cdf))

>csR <- AffymetrixCelSet$byName("CytoScanHD_Array", cdf=cdf)

>acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")

>csC <- process(acc, verbose=verbose)

print(csC)

> sessionInfo() 
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] aroma.light_2.4.0       aroma.affymetrix_2.14.0 affxparser_1.42.0      
[4] aroma.core_3.0.0        R.devices_2.13.2        R.filesets_2.10.0      
[7] R.utils_2.2.0           R.oo_1.19.0             R.methodsS3_1.7.0      

loaded via a namespace (and not attached):

 [1] matrixStats_0.50.1 codetools_0.2-14   listenv_0.6.0      future_0.10.0     
 [5] digest_0.6.8       R.huge_0.9.0       PSCBS_0.60.0       tools_3.2.2       
 [9] R.cache_0.12.0     parallel_3.2.2     base64enc_0.1-3    aroma.apd_0.6.0   
[13] R.rsp_0.21.0       globals_0.6.0      DNAcopy_1.42.0    

CEL format raw data are locate in "G:/rawData/CytoScanHD_Array/CytoScanHD_Array"

Looking forward your replay. Thank you very much.








Henrik Bengtsson

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Jan 13, 2016, 1:05:11 PM1/13/16
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On Sun, Jan 10, 2016 at 11:36 PM, <wxp...@gmail.com> wrote:
>
> Hi dear professor Henrik Bengtsson,
>
> When I was declaring the raw data set of CytoScan HD Array with aroma.affymetrix, I'm encountering the following errors:
>
> "Error: object 'csC' not found."

It seems like you didn't run the command before. Make sure each
object is actually created in every step by printing it, e.g.
print(cdf), etc. That should help you narrow down where your problem
is.

/Henrik
> Looking forward your replay. Thank you very much.
>
>
>
>
>
>
>
>
> --
> --
> 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.
>
>
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ali jan

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Nov 13, 2017, 7:29:07 PM11/13/17
to aroma.affymetrix
I tried your suggestion but it is still not working:

> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> # Don't display too many decimals.
> options(digits=4)
> cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/CytoScanHD_Array
Filename: CytoScanHD_Array.cdf
File size: 612.27 MiB (642007896 bytes)
Chip type: CytoScanHD_Array
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 2822125
Cells per unit: 2.44
Number of QC units: 4
> gi <- getGenomeInformation(cdf)
> print(gi)
UgpGenomeInformation:
Name: CytoScanHD_Array
Tags: na32,hg19,HB20111108
Full name: CytoScanHD_Array,na32,hg19,HB20111108
Pathname: annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,na32,hg19,HB20111108.ugp
File size: 13.46 MiB (14111425 bytes)
Chip type: CytoScanHD_Array
> si <- getSnpInformation(cdf)
> print(si)
UflSnpInformation:
Name: CytoScanHD_Array
Tags: na32,hg19,HB20111108
Full name: CytoScanHD_Array,na32,hg19,HB20111108
Pathname: annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,na32,hg19,HB20111108.ufl
File size: 5.38 MiB (5645047 bytes)
Chip type: CytoScanHD_Array
Number of enzymes: 1
> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
> print(acs)
AromaCellSequenceFile:
Name: CytoScanHD_Array
Tags: HB20111008
Full name: CytoScanHD_Array,HB20111008
Pathname: annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,HB20111008.acs
File size: 170.92 MiB (179217487 bytes)
Number of data rows: 6892960
File format: v1
Dimensions: 6892960x26
Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
Footer: <createdOn>20111108 21:44:22 PST</createdOn><platform>Affymetrix</platform><chipType>CytoScanHD_Array</chipType><srcFile><filename>CytoScanHD_Array.probe_tab</filename><filesize>409176930</filesize><checksum>beaaa56413608b3f9d9d464a07cddcae</checksum></srcFile><createdBy><fullname>Henrik Bengtsson</fullname><email>henrik.b...@aroma-project.org</email></createdBy>
Chip type: CytoScanHD_Array
Platform: Affymetrix
> csR <- AffymetrixCelSet$byName("CNV", cdf=cdf)
> print(csR)
AffymetrixCelSet:
Name: CNV
Tags: 
Path: rawData/CNV/CytoScanHD_Array
Platform: Affymetrix
Chip type: CytoScanHD_Array
Number of arrays: 460
Names: GSM1317174_H050150N-CytoScanHD_515-H050150N, GSM1317175_H050150T-CytoScanHD_516-H050150T, GSM1317176_H050154N-CytoScanHD_521-H050154N, ..., GSM1317635_H112971T-CytoScanHD_831-H112971T [460]
Time period: 2012-03-12 16:49:41 -- 2012-04-05 08:47:43
Total file size: 29.55 GiB
> cs <- csR
> par(mar=c(4,4,1,1)+0.1)
> plotDensity(cs, lwd=2, ylim=c(0,0.40))

> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
> print(acc)
AllelicCrosstalkCalibration:
Data set: CNV
Input tags: 
User tags: *
Asterisk ('*') tags: ACC,ra,-XY
Output tags: ACC,ra,-XY
Number of files: 460 (29.55 GiB)
Platform: Affymetrix
Chip type: CytoScanHD_Array
Algorithm parameters: {rescaleBy: chr "all", targetAvg: num 2200, subsetToAvg: int [1:6538333] 1 2 3 4 5 6 7 8 11 12 ..., mergeShifts: logi TRUE, B: int 1, flavor: chr "sfit", algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98}
Output path: probeData/CNV,ACC,ra,-XY/CytoScanHD_Array
Is done: FALSE
> print(csC)
Error in print(csC) : object 'csC' not found
> sessionInfo() 
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] aroma.light_3.8.0      aroma.affymetrix_3.1.0 aroma.core_3.1.1       R.devices_2.15.1       R.filesets_2.11.0      R.utils_2.5.0         
[7] R.oo_1.21.0            affxparser_1.50.0      R.methodsS3_1.7.1     

loaded via a namespace (and not attached):
 [1] matrixStats_0.52.2 codetools_0.2-15   listenv_0.6.0      future_1.6.2       digest_0.6.12      R.huge_0.9.0       PSCBS_0.63.0      
 [8] tools_3.4.2        R.cache_0.12.0     parallel_3.4.2     compiler_3.4.2     base64enc_0.1-3    aroma.apd_0.6.0    R.rsp_0.41.0      
[15] globals_0.10.3     DNAcopy_1.52.0    
> traceback()
No traceback available 

Henrik Bengtsson

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Nov 23, 2017, 6:41:23 PM11/23/17
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Still the same; you're not calling

csC <- process(acc, verbose=verbose)

321b...@gmail.com

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Nov 24, 2017, 3:18:31 PM11/24/17
to aroma.affymetrix
hello,have you solved your problem? I met the same error

在 2017年11月14日星期二 UTC+8上午8:29:07,ali jan写道:
Footer: <createdOn>20111108 21:44:22 PST</createdOn><platform>Affymetrix</platform><chipType>CytoScanHD_Array</chipType><srcFile><filename>CytoScanHD_Array.probe_tab</filename><filesize>409176930</filesize><checksum>beaaa56413608b3f9d9d464a07cddcae</checksum></srcFile><createdBy><fullname>Henrik Bengtsson</fullname><email>henrik.bengtsson@aroma-project.org</email></createdBy>

321b...@gmail.com

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Nov 24, 2017, 3:18:31 PM11/24/17
to aroma.affymetrix
hello , i called the csC <- process(acc, verbose=verbose) and them print(csC), it still met Error: object 'csC' not found.
在 2017年11月24日星期五 UTC+8上午7:41:23,Henrik Bengtsson写道:

Henrik Bengtsson

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Nov 24, 2017, 3:22:59 PM11/24/17
to aroma.affymetrix
If you called

   csC <- process(acc, verbose=verbose)

and csC is not found, then there was an error during that call that you must pay attention to.

/Henrik

PS. Are you a single person reporting via three different email addresses, or are you two (three?) different people having the same problem?
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