Hi Jason, So you can 1st verify that SOX6 is an "official" gene symbol (and not just a popular ALIAS) by checking that it is in the SYMBOL mapping. This is an important 1st step when dealing with gene symbols. "SOX6" %in% Rkeys(hthgu133aSYMBOL) [1] TRUE And it looks like it is. So then you can see if it is mapped or not with a line like you used: "SOX6" %in% mappedRkeys(hthgu133aSYMBOL) [1] FALSE And we can see that for the latest annotations it is not mapped to any probes. And here I can tell you that this it is very possible that SOX6 is not mapped today, but was mapped previously (with older annotations). The annotation mappings from Affymetrix change frequently and are updated to their latest versions with each release of bioconductor. This is because our knowledge of the genome and transcriptome represent a moving target, and the probes may not be detecting what they initially thought they would be detecting when the the chips were designed. It is NOT the case that the probes have changed, it's just that our understanding of what they are probably measuring has become a bit more refined. This is also one of the reasons why we ask that people install packages using biocLite(), because that helps to insure that the annotations packages you are using are the correctly matched set (something that becomes important when the annotations change frequently). So a likely interpretation is that SOX6 was thought to be measured by that probe and now it no longer is, OR possibly it is now one of multiple different genes that could potentially be detected by that set of probes and is being hidden by default as a result. For more information about how probes that map to multiple targets can be easily exposed, you might want to try out the toggleProbes() function. But here I can save you a little trouble though and tell you that for SOX6 at least, it appears that there are not presently any probes that are thought to detect it (according to the latest information we have from Affymetrix): allSymbs = toggleProbes(hthgu133aSYMBOL, "all") "SOX6" %in% mappedRkeys(allSymbs) [1] FALSE Hope this helps. Please let me know if you have more questions. Marc On 05/03/2011 09:26 AM, Jason Lu wrote: > Sorry. I was wrong. This gene is not mapped. >> aa = mappedRkeys(hthgu133aSYMBOL) >> "SOX6" %in% aa > [1] FALSE > > Jason > > > On Tue, May 3, 2011 at 12:22 PM, Jason Lu<jasonlu68 at="" gmail.com=""> wrote: >> Hi Andreas, >> >> I seems to be able to find this gene. >> >>> library(hthgu133a.db) >>> aa = Rkeys(hthgu133aSYMBOL) >>> "SOX6" %in% aa >> [1] TRUE >> >>> sessionInfo() >> R version 2.14.0 Under development (unstable) (2011-04-26 r55655) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] hthgu133a.db_2.5.0 org.Hs.eg.db_2.5.0 RSQLite_0.9-4 >> [4] DBI_0.2-5 AnnotationDbi_1.15.1 Biobase_2.13.1 >> >> loaded via a namespace (and not attached): >> [1] tools_2.14.0 >> >> >> Jason >> > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor