[BioC] Affy chip annotation changes

[James W. MacDonald]

On 11/1/2010 5:18 PM, Mark Cowley wrote:
> Hi Yuan, what does 244194_at map to in the annotation csv file from
> netaffx? There may be some discrepancy between the netaffx search
> engine&  the netaffx csv files.
>
> in these situations, I like to convince myself that affy's doing the
> right thing. Like Jim said, you could investigate further using
> various R tools listed below, or, if you haven't used those tools
> before, then for about 10 minutes work, you can align the 25mer
> probes for each probeset (which you can get from netaffx) to the
> genome using BLAT at the UCSC genome browser. This will tell you
> whether the probes will target ADAM22 or not.

I have a little function that I use to do this sort of thing:

blatGene <- function(affyid, probe, filename){
     ## affyid == Affy probeset ID
     ## probe == BioC probe package name
     ## filename == output file name
     require(probe, quietly = TRUE, character.only = TRUE)
     tmp <- data.frame(get(probe))
     if(length(affyid) > 1){
         seqnc <- vector()
         for(i in seq(along = affyid))
             seqnc <- c(seqnc, tmp[tmp$Probe.Set.Name == affyid[i], 1])
     }else{
         seqnc <- tmp[tmp$Probe.Set.Name == affyid,1]
     }
     out <- vector()
     if(length(seqnc) > 25) warning("Blat will only return values for 25 
or fewer sequences!",
                                    call. = FALSE)
     for(i in seq(along = seqnc)) out <- rbind(out, rbind(paste("> 
Probe", i, sep=""), seqnc[i]))
     write.table(out, filename, sep="\t", quote=FALSE, row.names=FALSE, 
col.names=FALSE)
}

I used this to look at the two probesets that apparently no longer 
target ADAM22, and for hg18 both probesets are off the 3' end of the gene.

Best,

Jim


>
> HTH Mark
>
> On 02/11/2010, at 1:42 AM, Yuan Hao wrote:
>
>> Hi Jim and Martin,
>>
>> Thank you very much for your reply! I have a feeling that this
>> question is too vague to be answered unless down to the very end of
>> chip design. However, just for you information. I actually checked
>> these two missing probe sets on NetAFFX from the Affymetrix
>> website, and one of them, "244194_at", seems still linking to
>> ADAM22, while another is not any more.
>>
>> Regards, Yuan
>>
>> I actually checked on NetAffx from the affymetrix website for two
>> missed probe sets corresponding to ADAM22. "2 On 1 Nov 2010, at
>> 14:05, James W. MacDonald wrote:
>>
>>> Hi Yuan,
>>>
>>> The annotation packages we provide are simply a re-packaging of
>>> data that we get from Affymetrix, so the simple answer is that
>>> Affy decided that two of those probesets don't really interrogate
>>> the transcript for that gene.
>>>
>>> You could investigate this further by either going to the
>>> Affymetrix website and downloading the most recent annotation csv
>>> file, and the csv file that was contemporaneous with the older
>>> annotation package (2.2.11), and comparing the two. This will
>>> likely not be that enlightening, as I would bet the annotation
>>> simply changes for the two probesets that no longer point to
>>> ADAM22.
>>>
>>> You could also investigate further using e.g., the rtracklayer,
>>> Biostrings, and BSgenome.Hsapiens.UCSC.hg17
>>> (BSgenome.Hsapiens.UCSC.hg19) packages.
>>>
>>> Best,
>>>
>>> Jim
>>>
>>>
>>>
>>> On 11/1/2010 7:14 AM, Yuan Hao wrote:
>>>> Dear list,
>>>>
>>>> I've downloaded two versions of hgu133plus2 array annotation
>>>> package: v2.2.11(R 2.9.2) and v2.4.5 (R 2.12.0). Some probe
>>>> sets annotated in the former version are no longer supported in
>>>> the recent version. For example, "ADAM22" was annotated by
>>>> eight probe sets ("1555024_at" "206615_s_at" "206616_s_at"
>>>> "208226_x_at" "208227_x_at" "208237_x_at" "213411_at"
>>>> "244194_at"), which have been reduced to six in the latest
>>>> annotation (the last two probe sets have been missing). I would
>>>> be grateful if someone could provide some insight about it,
>>>> especially for this case!
>>>>
>>>> Regards, Yuan
>>>>
>>>> _______________________________________________ Bioconductor
>>>> mailing list Bioconductor at stat.math.ethz.ch
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>>>
>>>
>>>>
-- 
>>> James W. MacDonald, M.S. Biostatistician Douglas Lab University
>>> of Michigan Department of Human Genetics 5912 Buhl 1241 E.
>>> Catherine St. Ann Arbor MI 48109-5618 734-615-7826
>>> **********************************************************
>>> Electronic Mail is not secure, may not be read every day, and
>>> should not be used for urgent or sensitive issues
>>
>> _______________________________________________ Bioconductor
>> mailing list Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the
>> archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues