I was working with the cytoScan HD chiptype to preprocess the .CEL files
But was inturrupted with the following error.
following are my log results:
> 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$byChipType(getChipType(cdf, fullname=FALSE))
> print(acs)
AromaCellSequenceFile:
Name: CytoScanHD_Array
Tags: HB20111008
Full name: CytoScanHD_Array,HB20111008
Pathname:
annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,HB20111008.acs
File size: 170.92 MiB (179217487 bytes)
Number of data rows: 6892960
File format: v1
Dimensions: 6892960x26
Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1
Footer: <createdOn>20111108 21:44:22
PST</createdOn><platform>Affymetrix</platform><chipType>CytoScanHD_Array</chipType><srcFile><filename>CytoScanHD_Array.probe_tab</filename><filesize>409176930</filesize><checksum>beaaa56413608b3f9d9d464a07cddcae</checksum></srcFile><createdBy><fullname>Henrik
Bengtsson</fullname><email>henrik.bengts...@aroma-project.org</email></createdBy>
Chip type: CytoScanHD_Array
Platform: Affymetrix
>
> csR <- AffymetrixCelSet$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
>csC <- process(acc, verbose=verbose)
>print(csC)
Error in print(csC) : object 'csC' not found
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