Question

Regarding Microarray Data

3

Entering edit mode

12.9 years ago

Nitish Kumar ▴ 30

Hi,

I am new one in microarray analysis.

I have 388 .CEL file for one GEOID. I have normalized it with GCRMA package. Now I want to convert probe wise intensity into Gene-wise. I mean instead to probe id I want to use Gene ID. Can any one suggest me how I can convert this normalized prove intensity into gene intensity. Is there any module/command in Bioconductor.

Thanks in advanced.

bioconductor microarray data • 2.7k views

ADD COMMENT • link updated 12.9 years ago by Will 4.5k • written 12.9 years ago by Nitish Kumar ▴ 30

4

Entering edit mode

There are several different strategies, but first, what exact array platform are you using? M430, Gene 1.0, etc?

ADD REPLY • link 12.9 years ago by David Quigley 11k

score 5 · Answer 1 · 2011-05-25

I would suggest re-normalizing with a custom cdf. Whichever program you used to do the original RMA normalization will work easily with these. The BrainArray group has created one for each affy chip which creates unique probesets for each gene-id. They have cdfs which map to unique UNIPROTS, Entrez-ids, refseqs and just about anything else you can think of.