Hi,
Whilst looking at a dataset just now, I was searching for a couple of critical gene symbols, and couldnt find them.
grep("Foxp3",unlist(as.list(mta10sttranscriptclusterSYMBOL))) integer(0) grep("Foxp3",unlist(as.list(mta10sttranscriptclusterGENENAME))) integer(0) grep("Gata3",unlist(as.list(mta10sttranscriptclusterSYMBOL))) integer(0) grep("Gata3",unlist(as.list(mta10sttranscriptclusterGENENAME))) integer(0)
I have the latest version for the mta10sttranscriptcluster.db package, as far as I am aware:
sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-unknown-linux-gnu (64-bit)
...
other attached packages: [1] mta10sttranscriptcluster.db_8.3.1 org.Mm.eg.db_3.1.2 [3] pd.mta.1.0_3.12.0 oligo_1.32.0 [5] Biostrings_2.36.1 XVector_0.8.0 [7] oligoClasses_1.30.0 GOstats_2.34.0 ...
To check they were actually on the array in the first place, I went to the Affymetrix www site and downloaded their annotation (MTA-1_0.na35.mm10.transcript.csv) and looked there:
egrep -m2 -i "gata3|foxp3" MTA-1_0.na35.mm10.transcript.csv | cut -d "," -f1,2,3,4,5,6,7,8
"TC0200002935.mm.1","TC0200002935.mm.1","chr2","-","9857078","9890034","248","NM_008091 // Gata3 ....
"TC0X00000058.mm.1","TC0X00000058.mm.1","chrX","+","7573600","7595243","241","NM_001199347 // Foxp3 ...
So, it seems that for some wierd reason, these loci didnt make it into the Bioc annotation package for this array! I havent checked for any other genes. Would it be possible to update the package please?
Many thanks, cheers!
Al
But is it surprising that they are not present in the traditional maps?
Not really. The reason we (Marc Carlson and I, primarily) keep trying to shove people towards the new select() interface is that the old maps return NA for multi-mapping probes:
Old habits die hard, and there is a wealth of easily Googleable web pages that will give naive users the idea that
is 'the way to go' rather than 'an archaic thing to do, left over for backwards compatiblity'.