[Bioc-devel] hgu95aprobe missing sequences

James W. MacDonald jmacdon at med.umich.edu
Thu Jul 12 21:33:52 CEST 2007

Actually, I should have checked closer. The probe_tab file you can get 
from Affy now does contain these sequences, even if Netaffx still points 
you to TIGR. We don't as a rule re-download all these probe_tab and cdf 
files when we build the annotation files for each release, as they are 
in general static documents. The end result being that when I built the 
probe packages the last time I used an old version of the probe_tab 
files for the hgu95a, hgu95av2, and hg110 probe packages that didn't 
contain these sequences.

I will download the new probe_tab files and rebuild. The rebuilt 
packages should make it to the release repositories in the near future.



James W. MacDonald wrote:
> Hi Ernest,
> The reason some of the probesets are not found in the probe package is 
> because they are not available from Affy, and so are not in the probe 
> data file that we use to build the probe package. This is because Affy 
> got these sequences from TIGR, and evidently are not at liberty to 
> release the sequences. Here is an example from Netaffx showing that 
> they don't give out the sequence, but tell you to get it from TIGR:
> https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=HG-U95AV2%3A1142_AT 
> Best,
> Jim
> Ernest Turro wrote:
>> On 12 Jul 2007, at 14:52, Seth Falcon wrote:
>>> sessionInfo() please?
>>> -- 
>>  > sessionInfo()
>> R version 2.5.0 (2007-04-23)
>> i386-apple-darwin8.9.1
>> locale:
>> C
>> attached base packages:
>> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"      
>> "datasets"
>> [7] "methods"   "base"
>> other attached packages:
>>    hgu95acdf hgu95aprobe matchprobes        affy      affyio     Biobase
>>     "1.16.0"    "1.16.2"     "1.8.1"    "1.14.1"     "1.4.0"     
>> "1.14.0"
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

More information about the Bioc-devel mailing list