Question: What package should I use to retrieve chromosome location for Affymetrix id of gene symbol id while doing gene expression microarray analysis ?
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gravatar for anandprem1792
24 months ago by
anandprem179210 wrote:

Can anyone please tell me how to retrieve chromosome location for a set of gene id

ADD COMMENTlink modified 24 months ago by James W. MacDonald52k • written 24 months ago by anandprem179210
Answer: What package should I use to retrieve chromosome location for Affymetrix id of g
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gravatar for James W. MacDonald
24 months ago by
United States
James W. MacDonald52k wrote:

It's a two-step process.

egids <- select(<ChipDb package goes here>, keys(<ChipDb>), "ENTREZID")

chrlocs <- select(<OrganismDb or TxDb package>, as.character(egids[,2]), c("CDSCHROM","CDSSTART","CDSEND"), "ENTREZID")

You will have to figure out what ChipDb and OrganismDb or TxDb package you need, because you are being unnecessarily mysterious about what you are doing. Asking vague questions will either get you a vague answer, or none at all, so in future you should try to be more specific.

ADD COMMENTlink written 24 months ago by James W. MacDonald52k
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