Convert Probes Into Genes

Question

[silkeverhelle]

Hi, I retrieved R data from insilicoDB (gse10315, which is normalized). If we want to use this in MeV to make a heatmap, we see that we have probes instead of genes. We want to convert these probes into genes. How can we do this? Thanks!

Answer 1

[B. Arman Aksoy]

GEO provides platform details for each data set that it hosts. For your case, for example, if you go to the data-set page:

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10315

and then click on the platform name (GPL570), which will take you to his page:

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570

You can download the annotation file that contains the probe name to gene name/id mapping from this page (see the "Download Full Table" button near the end of the page).

You can then use this file and using R's aggregate function merge multiple probes based on their gene symbols/ids to get you gene-centric matrix.