Different annotation obtained from hgu133a2.db and affymetrix annotation release
I've got a lncRNA NEAT1, and I want to see its expression in one dataset from hgu133a2 platform. I found the affymetrix id '214657_s_at' was mapped to NEAT1 in affymetrix annotation release 'HG-U133A_2 Annotations, CSV format, Release 36 (19 MB, 4/13/16)'. But when I query the probeset using the following code
getEG('214657_s_at', 'hgu133a2.db')
I got an NA return. I'm wondering the difference between hgu133a2.db and the annotation release from affymetrix. Should I continue to use affymetrix annotation instead of hgu133a2.db?
• 1,287 views
•
link
updated
by
Biostar
•
written
by
2323982403 •
•
written
by
2323982403 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
TSS Enrichment error in Signac
written by kousi31 •
-
vcfnulldotslashdot Type-Error: can't multiply sequence by non-int of type 'float'
written by johanna.pieplow •
-
Should Affymetrix probe annotation include only specific gene biotypes?
written by Aspire
-
How to annotate probes to a GEO serie matrix?
written by pablojosegiraudi •
-
Ensembl/SGD Alternative gene isoforms / splice variantes for S. cerevisiae
written by jmat •
-
How to identify lncRNAs from a probe set?
written by dz2353
-
Using microarray re-annotation to combine array and Chip-Seq data
written by 2323982403 •
-
Strange esearch behavior
written by Ram
-
how to use custom cdf in R to convert affyID to gene symbol?
written by Raheleh
-
Affymetrix Genechip Probeset Id Question In General And Using R
written by Sandra •
Indeed, I never use those annotation DBs because they are frequently out of date. If I want the latest information, I take it direct from Affymetrix's website.