[BioC] gene SOX6 in HT HG-U133A
Marc Carlson
mcarlson at fhcrc.org
Tue May 3 19:14:26 CEST 2011
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
More information about the Bioconductor
mailing list