Question About Affymetrix Array:Ht-Hg-U133Acdf

Question

[Richard]

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

[Neilfws]

Reformatted your question to make it readable. Please note for future reference (in particular, indent lines of code using 4 spaces).

[David Quigley]

What's the GEO ID of the dataset you downloaded? Are you completely sure it's 133A and not HG95?