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$byChipType(getChipType(cdf, fullname=FALSE))
> print(acs)
AromaCellSequenceFile:
Name: CytoScanHD_Array
Tags: HB20111008
Full name: CytoScanHD_Array,HB20111008
Pathname:
annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,HB20111008.acs
File size: 170.92 MiB (179217487 bytes)
Number of data rows: 6892960
File format: v1
Dimensions: 6892960x26
Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1
Footer: <createdOn>20111108 21:44:22
PST</createdOn><platform>Affymetrix</platform><chipType>CytoScanHD_Array</chipType><srcFile><filename>CytoScanHD_Array.probe_tab</filename><filesize>409176930</filesize><checksum>beaaa56413608b3f9d9d464a07cddcae</checksum></srcFile><createdBy><fullname>Henrik
Bengtsson</fullname><email>[email protected]</email></createdBy>
Chip type: CytoScanHD_Array
Platform: Affymetrix
>
> csR <- AffymetrixCelSet$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
On Wednesday, January 13, 2016 at 11:05:11 PM UTC+5, Henrik Bengtsson wrote:
>
> On Sun, Jan 10, 2016 at 11:36 PM, <[email protected] <javascript:>> 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
>
> >
> > 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.
> >
> >
> >
> >
> >
> >
> >
> >
> > --
> > --
> > 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 [email protected]
> <javascript:>
> > To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
> >
> > ---
> > You received this message because you are subscribed to the Google
> Groups "aroma.affymetrix" group.
> > To unsubscribe from this group and stop receiving emails from it, send
> an email to [email protected] <javascript:>.
> > For more options, visit https://groups.google.com/d/optout.
>
--
--
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 [email protected]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
---
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to [email protected].
For more options, visit https://groups.google.com/d/optout.
