Question: Microarray: aroma.affymetrix version for HuGene and HuExon
0
gravatar for Bioinformatics_NewComer
3 months ago by
Genomic Island
Bioinformatics_NewComer320 wrote:

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?

aroma microarray expression • 197 views
ADD COMMENTlink modified 3 months ago by Kevin Blighe37k • written 3 months ago by Bioinformatics_NewComer320
2
gravatar for Kevin Blighe
3 months ago by
Kevin Blighe37k
Republic of Ireland
Kevin Blighe37k wrote:

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

ADD COMMENTlink written 3 months ago by Kevin Blighe37k
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