[BioC] gene SOX6 in HT HG-U133A

[Marc Carlson]

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
>>
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