Dear Henrik,
I ran "doCRMAv2" with copy number data on the GenomeWide SNP6.0
platform.
For your information, all annotation files used in this run were
downloaded from your website, and R 2.13.0 was loaded.
This run generated a warning message as follows:
>ds <- doCRMAv2(csR, cdf=cdf, verbose=verbose);
Warning messages:
1: In structure(list("doCRMAv2(subcsR, cdf = cdf, verbose = verbose)"
= <environment>, ... :
Rcache file format error (''~/.Rcache/aroma.affymetrix/
5c65e4c63c15e1375fd8bd2809ad6fe1.Rcache' [description of the opened
connection]'). Invalid identifier: &
2: In log2(y) : NaNs produced
3: In log2(y) : NaNs produced
Even though it is not an error message, I am not sure whether or not I
can discard this warning message.
I will appreciate it if you let me whether I can use the outputs from
this run for any future analysis, or I need to re-run it with
appropriate settings.
Thank you very much,
Hoon
P.S. The codes I ran were the following:
#-----------------------------------------------------------------------
>dataSet <-"mytest";
>chipType <-"GenomeWideSNP_6";
>tags <-"Full";
>library(aroma.affymetrix)
>verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
>options(digits=4);
>cdf <-AffymetrixCdfFile$byChipType(chipType, tags=tags);
>print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/GenomeWideSNP_6
Filename: GenomeWideSNP_6,Full.cdf
Filesize: 470.44MB
Chip type: GenomeWideSNP_6,Full
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 1881415
Cells per unit: 3.66
Number of QC units: 4
>gi <- getGenomeInformation(cdf)
>print(gi)
UgpGenomeInformation:
Name: GenomeWideSNP_6
Tags: Full,na30,hg18,HB20100215
Full name: GenomeWideSNP_6,Full,na30,hg18,HB20100215
Pathname: annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,Full,na30,hg18,HB20100215.ugp
File size: 8.97 MB (9407867 bytes)
RAM: 0.00 MB
Chip type: GenomeWideSNP_6,Full
>si <- getSnpInformation(cdf)
>print(si)
UflSnpInformation:
Name: GenomeWideSNP_6
Tags: Full,na30,hg18,HB20100215
Full name: GenomeWideSNP_6,Full,na30,hg18,HB20100215
Pathname: annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,Full,na30,hg18,HB20100215.ufl
File size: 7.18 MB (7526452 bytes)
RAM: 0.00 MB
Chip type: GenomeWideSNP_6,Full
Number of enzymes: 2
>csR <-AffymetrixCelSet$byName(dataSet, cdf=cdf);
>ds <- doCRMAv2(csR, cdf=cdf, verbose=verbose);
Warning messages:
1: In structure(list("doCRMAv2(subcsR, cdf = cdf, verbose = verbose)"
= <environment>, ... :
Rcache file format error (''~/.Rcache/aroma.affymetrix/
5c65e4c63c15e1375fd8bd2809ad6fe1.Rcache' [description of the opened
connection]'). Invalid identifier: &
2: In log2(y) : NaNs produced
3: In log2(y) : NaNs produced
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.affymetrix_2.2.0 affxparser_1.24.0 aroma.apd_0.2.0
[4] R.huge_0.3.0 aroma.core_2.2.0 aroma.light_1.22.0
[7] matrixStats_0.4.0 R.rsp_0.6.2 R.cache_0.5.2
[10] R.filesets_1.1.0 digest_0.5.1 R.utils_1.8.2
[13] R.oo_1.8.2 R.methodsS3_1.2.1
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