Question: Question About Affymetrix Array:Ht-Hg-U133Acdf
2
gravatar for Richard
7.6 years ago by
Richard20
Richard20 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

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

affymetrix • 2.4k views
ADD COMMENTlink modified 7.6 years ago by Neilfws48k • written 7.6 years ago by Richard20

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

ADD REPLYlink written 7.6 years ago by Neilfws48k

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

ADD REPLYlink written 7.6 years ago by David Quigley11k
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