I'm trying to use some cancer cell line data from the paper "Systematic identification of genomic markers of drug sensitivity in cancer cells":
The title says that it is HT-HGU133a V2; but the array accession linked to it says it's the HT-HGU133a. I thought that some probes/layout had been changed between the U133a and U133a2 chips? I want to be able to add in our cell line data that was on the HGU133a V2 platform.
I then found this BioC thread that seemed to say that the annotation to use would be hgu133a2, but that a separate annotation was made for hthgu133a to 'reduce' confusion:
But I'm still confused! When I load the raw CEL files and then normalize it with the different CDFs (hthgu133a vs. hgu133a2) I get completely different results; the normalized expression values for a single sample normalized with the different CDFs have absolutely no correlation. It makes me think that the layout is somehow different! Though, in the resulting ExpressionSets the probes are in the same order and exactly match. Can anyone offer a suggestion, or is there a way that I can compare the layout for the chips?
I actually also tried this in Partek; it failed when I manually changed the annotation to use to HGU133a V2 (said that the dimensions were incorrect).