Error: object 'csC' not found.

[wxp...@gmail.com]

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]

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.
>
>
>
>
>
>
>
>

> --
> --
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>
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[ali jan]

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]

Still the same; you're not calling

csC <- process(acc, verbose=verbose)

[321b...@gmail.com]

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]

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]

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?