Working with rice affymetrix chip in R
Hi
I am working on a microarray study with data from a Rice AffyMetrix chip. I have done a differential expression analysis, giving me a list of AffyMetrix probe ids. I would like to convert these to Entrez Gene Ids using R. Is this possible?
Thanks for your help!
• 2,214 views
•
link
updated
by
Biostar
•
written
by
lippeveld.maxim •
•
written
by
lippeveld.maxim •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Converting NCBI Entrez ID to Glyma ID
written by Bioinf_Questions •
-
constructing a reference matrix from affy 2.0 chip for a 4.0 chip.
written by RNAseqer
-
how to get gene symbol from Entrez id
written by parinv •
-
"old" microarray probe IDs conversion to genes
written by irene768 •
-
Apple gene ID conversion tool
written by rj.rezwan •
-
Meta_analysis of different platforms of microarray data
written by j_jamal96 •
-
Filtering low intensity probes of microarray data
written by prathyushareddy87 •
-
Generic probe IDs to HUGO IDs API
written by ncl.lazzarini
-
Use Affymetrix Gene Expression Data in Cytoscape
written by daniel.rapoport •
-
Microarray Gene Annotation
written by Harsh •
The way to do this in R would be to check if there is an annotation package for the Affymetrix rice chip in Bioconductor, although I've had a quick look, and I couldn't find one.
You could try BioMart.
Otherwise, the best thing to do is to get the latest version of the Affymetrix annotations from the technical documentation on the Affymetrix website.
Great, thank you! I ended up using the rice annotation file from affymetrix.