This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Affymetrix cross platform probe matching

Hi all,

I have multiple datasets some from hgu133plus2 ( GPL570) and one affymetrix human exon array 1.0st. I wanna compare the DEGs from these two platforms. Is there any cross platform probe matching data for affymetrix or any suggestions to deal with multiple probesets hitting same gene problem?

Thanks in advance

microarray affymetix
• 1,173 views • link
written by gracie • gracie

1 answer

Hello, can you please elaborate on what you mean by 'compare'? - do you mean to merge the datasets or to perform a meta-analysis?

• 0 views • link
written by Kevin Blighe Kevin Blighe

Clustering based on DEGs basicly and also extracting the genes altered same and opposite direction. I am not planing to do meta analysis because each dataset contains their own control group and I am only intrested in DEGs.

• 0 views • link
written by gracie • gracie

Okay, I would convert the probe identifiers to a common annotation type and then go by that. For example, convert to HGNC symbols or Ensembl gene IDs.

• 0 views • link
written by Kevin Blighe Kevin Blighe

Log in to answer this question.

More posts like this