Regarding Microarray Data
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12.8 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
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There are several different strategies, but first, what exact array platform are you using? M430, Gene 1.0, etc?

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12.8 years ago
Will 4.5k

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.

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