Microarray: aroma.affymetrix version for HuGene and HuExon

Question

[Bioinformatics_NewComer]

Hi All,

I'm using aroma.affymetrix R package to get exon level summaries. HuEx-1_0-st-v2 CDF file
I got exon level estimates from instructions at:

http://www.aroma-project.org/chipTypes/HuGene-1_0-st-v1/

I cannot get transcript level information (FIRMA scores) working hence I would like to have gene level estimates.

For gene level summaries for which I got HuGene-1_0-st-v1 r4 CDF file.

I've V1 for HuGene and V2 for HuEx. Would that be an issue for downstream analysis?

Answer 1

[Kevin Blighe]

I would just use the oligo R package and not aroma.affymetrix. Oligo will automatically detect the chip type and obtain the necessary system info.

To produce gene- or exon-level expression values, see my answer here: A: How to map probeset associated statistics to gene statistics in microarray diffe

Kevin