Question: Regarding Microarray Data
3
gravatar for Nitish Kumar
7.9 years ago by
Nitish Kumar30
Nitish Kumar30 wrote:

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.

data bioconductor microarray • 1.7k views
ADD COMMENTlink modified 7.9 years ago by Will4.5k • written 7.9 years ago by Nitish Kumar30
4

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

ADD REPLYlink written 7.9 years ago by David Quigley11k
5
gravatar for Will
7.9 years ago by
Will4.5k
United States
Will4.5k wrote:

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.

ADD COMMENTlink written 7.9 years ago by Will4.5k
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