Hi, I just received some RNA expression data measured with the Affymetrix HuGene 2.0ST array. When trying to summarize the probesets using R or Affymetrix Power Tools I am required to input a cdf file. I was looking all over the internet to find 'the official cdf file' for this array.Is it possible that affymetrix did not make this HuGene 2.0 ST cdf file publicly available? I found an unsupported cdf file but I was just wondering what everyone else is doing to analyze the HuGene 2.0ST array. Thanks
When you consider to use Affymetrix Power Tools instead of R you don't need a CDF file. Use the "Library Files" for the HuGene 2.1 ST Array from the Affymetrix web sites instead and run the power tools with a command similar to that one:
apt-probeset-summarize -m transript_cluster.mps -a rma-sketch -p chip.pgf -c chip.clf -o output-dir *.cel
You will need to look for it on the Affymetrix website and/or ask for assistance via their customer support in case this info ends up well hidden from view - as it often happens.
You can find "unofficial" CDF files at this link. Scroll down to section 4, "Affymetrix-derived CDF (and .DB) R-environments AND binary CDFs for the gene ST arrays and the GeneTitan plates."
This may be the unsupported file that you mentioned in the question. If so - it seems to be the best (only) option at present.
Bioconductor also provides a platform design annotation package which might be of use.
Is there any option to annotate Affymetrix Hugene 2.0St Array Id for coding genes using R. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
gset <- getGEO("GSE", GSEMatrix =TRUE, AnnotGPL=FALSE)
Log in to answer this question.
