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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anandprem1792 ▴ 20

@anandprem1792-13905

Last seen 7.0 years ago

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

affymetrix microarrays differential gene expression • 959 views

ADD COMMENT • link updated 7.0 years ago by James W. MacDonald 67k • written 7.0 years ago by anandprem1792 ▴ 20

score 0 · Answer 1 · 2017-12-11

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.