I'm analyzing some Human Exon Arrays from Affymetrix, from a pilot study, with oligo package, at transcript (core) level.
For the samples analyzed, I have some phenoData, as the expression levels (low / high, obtained by qRT-PCR) and mutational status of some genes. As it's a pilot study with very few number of chips, and unbalanced group sizes, I was asked to check whether these genes whose expression levels where known to be different, were actually differentialy expressed in the arrays.
The problem is that one of the genes I had to check has no annotation in pd.huex.1.0.st.v2 (I'm using pd.huex.1.0.st.v2_3.12.0). I checked for this gene in NetAffx Center, in order to know whether it was not represented in the array, or it has not been annotated, and I've found that there is a transcript cluster ID associated with the gene, and there's annotation. So, I've downloaded the last Affymetrix annotation at transcript level file (HuEx-1_0-st-v2.na35.hg19.transcript file) and the transcript cluster is now annotated, althought it wasn't there at least in the one I used when the arrays were firstly analyzed, with Affymetrix TAC Software, HuEx-1_0-st-v2 Transcript Cluster Annotations, CSV, Release 33.1.
So, I have two questions:
1) Is it possible for me to generate a pd.huex.1.0st annotation file based on the last annotation files from Affymtrix that could be integrated in the oligo workflow for analyzing these chips? how can oligo be said to use this file, instead of the one generated by Mr. Benilton Carvalho?
2) Is it possible to know the version of affymetrix annotation files used to generate pd.huex.1.0.st.v2_3.12.0?
Thank you in advance