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ali jan

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Nov 13, 2017, 7:01:26 PM11/13/17

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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.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}