Hi.
On Tue, Dec 13, 2011 at 7:48 AM, wisekh6 <wise...@gmail.com> wrote:
> 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: &
Shouldn't be a problem, because cached ("memoized") files that cannot
be read are ignored, and are instead recomputed.
Though, I'm curious why you get that; could you send me that *.Rcache
file (offline), so I can have a look at it?
> 2: In log2(y) : NaNs produced
> 3: In log2(y) : NaNs produced
These are alright, because they occur when taking the log of negative
values, which can happen for very weak signals that have been
background corrected.
/Henrik
>
> 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
>
> --
> 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.
>
>
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--
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.
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