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!