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,HB2008
Full name: CytoScanHD_Array,na32,hg19,HB2008
Pathname:
annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,na32,hg19,HB2008.ugp
File size: 13.46 MiB (14111425 bytes)
Chip type: CytoScanHD_Array
>
> si <- getSnpInformation(cdf)
> print(si)
UflSnpInformation:
Name: CytoScanHD_Array
Tags: na32,hg19,HB2008
Full name: CytoScanHD_Array,na32,hg19,HB2008
Pathname:
annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,na32,hg19,HB2008.ufl
File size: 5.38 MiB (5645047 bytes)
Chip type: CytoScanHD_Array
Number of enzymes: 1
>
> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
> print(acs)
AromaCellSequenceFile:
Name: CytoScanHD_Array
Tags: HB20111008
Full name: CytoScanHD_Array,HB20111008
Pathname:
annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,HB20111008.acs
File size: 170.92 MiB (179217487 bytes)
Number of data rows: 6892960
File format: v1
Dimensions: 6892960x26
Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1
Footer: 2008 21:44:22
PSTAffymetrixCytoScanHD_ArrayCytoScanHD_Array.probe_tab409176930beaaa56413608b3f9d9d464a07cddcaeHenrik
Bengtssonhenrik.bengts...@aroma-project.org
Chip type: CytoScanHD_Array
Platform: Affymetrix
>
> csR <- AffymetrixCelSet$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.1252LC_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_1.21.0affxparser_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_3.4.2R.cache_0.12.0 parallel_3.4.2
compiler_3.4.2 base64enc_0.1-3aroma.apd_0.6.0R.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, > 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), et
