[BioC] question about affymetrix array:ht-hg-u133acdf

[James W. MacDonald]

Hi Richard,

On 10/14/2011 7:03 AM, Richard [guest] wrote:
> hello,everyone!
> I found a question when processing the affymetrix microarray data that I downloaded from NCBI. I had suffered from this question for two dayes, and I couldn't find useful information from the internet.
>
> the affymetrix array i processed was ht-hg-u133acdf. And the R code was:
> -----------------------------------------
> #!/usr/bin/env Rscript
> library("methods")
> library("Biobase")
> library("affy")
> library("genefilter")
> library("gcrma")
> library("simpleaffy")
> library("xtable")
> library("preprocessCore")
> library("affyPLM")
> library("RColorBrewer")
> library("lattice")
> library("affyQCReport")
> library("hthgu133acdf")
> work.data<-ReadAffy("GSM637758.cel","GSM637759.cel","GSM637800.cel")
> QCReport(work.data,file="t.pdf")
> ------------------------------------------
>
> Then R give me thus information(Sorry some sentences were translated):
> ------------------------------------------
> error at plot(qc(object)) :
>    something was wrong of function 'plot'when evaluating parameter 'x',at  setCEnvironment(cdfn) :
>    Could not find array definition file ' hthgu133acdf.qcdef '. Simpleaffy does not know the QC parameters for this array type.
> See the package vignette for details about how to specify QC parameters manually

This above line is the hint you seem to have missed. There is no set of 
QC parameters for this particular chip, so you have to create some 
yourself. The instructions in the vignette are a bit terse, so here is a 
hint.

The HT-HG-U133a chip is very similar to the 'regular' HG-U133a chip, and 
there is already a set of QC parameters for the latter chip in the 
simpleaffy package. So you could create a slightly modified version of 
that file, renaming it accordingly, and it should all work.

cd /path/to/R/library/simpleaffy/extdata
sed 's/hgu133acdf/hthgu133acdf/' hgu133acdf.qcdef > hthgu133acdf.qcdef

Best,

Jim


> ------------------------------------------
>
> I got the information of the variable "work.data" in R:
> ----------------------------------------
>   AffyBatch object
> size of arrays=744x744 features (17 kb)
> cdf=HT_HG-U133A (22277 affyids)
> number of samples=3
> number of genes=22277
> annotation=hthgu133a
> ------------------------------------------
>
> I tried to solve this problem by all means:
> changing the qc environment:setQCEnvironment("hthgu133acdf");
> remove the "hthgu133acdf" package, then reinstall it;
> updating the version of R from 2.10 to 2.13.2, then reinstall all the packages needed;
> searching the google, a few questions that were similar were found, but no answers suitable.
> when I changed the array data to "hgu133acdf" or "hgu95av2", everything was OK! So i don't know if there is some problem with that package,or anyone could help me solve this question!
>
> thanks
>
>   -- output of sessionInfo():
>
> R version 2.13.2 (2011-09-30)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=zh_CN.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=zh_CN.UTF-8        LC_COLLATE=zh_CN.UTF-8
>   [5] LC_MONETARY=C              LC_MESSAGES=zh_CN.UTF-8
>   [7] LC_PAPER=zh_CN.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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