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 ------------------------------------------ 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.

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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues