[BioC] error in hugene10sttranscriptcluster

[James W. MacDonald]

Hi Javier,

On 4/18/2011 7:02 AM, Javier Pérez Florido wrote:
> Dear Jim,
> Thanks for your quick reply.
> I'm not sure if I understood your explanation. I did some research at
> the netaffx annotation as you suggested.
>
> I've summarized using oligo package at the "core" level, i.e. transcript
> level. I've checked through NetAffx annotation files all the transcript
> clusters related to the NR_002716 gene.
> These are: 7948894, 8019631,8019633,8019635,8019637,8019639, 8019641,
> 8019703,8019705,8019707,8019709 and 8019802. What does this mean? A gene
> is made up of several clusters? Is the gene repeated through these
> clusters? Once I understand this issue, I will understand how limma
> works on these arrays, since I don't know whether cluster=gene or
> clusterS = gene.

This is one of the problems inherent to the design of arrays that use 
really short probes (and often very few probes per probeset). Since the 
probes are so short, they sometimes will bind to many different 
transcripts, so it is hard to say which transcript is responsible for 
the signal for a given probeset.

If you put 8019631 in netaffx, you will see that the hybridization 
target is 'mixed', meaning it binds multiple transcripts. The only 
probeset that comes up if you query netaffx for NR_002716 is 7948894, so 
I assume all the others you note are mixed as well.

>
> I observed some differences between the annotated files
> HuGene-1_0-st_v1.na29.hg18.transcript (the one I used before) and
> HuGene-1_0-st_v1.na31.hg19.transcript (the latest one). The main
> differences are related to the "start" and "stop" fields on these files
> for each of the transcript clusters described above.
> For the first version (na29.hg18), there are numbers different from zero
> on these fields, whereas in the latest version (na31.hg19), the "start"
> and "stop" values are zero. However, in both files, the "gene
> assignment" field is NR_002716. So, I don't understand why when I use
> mget("8019631",hugene10sttranscriptclusterACCNUM) and error is found
> whereas in the NetAffx annotation file this accession number exists.

For the annotation packages we supply (we meaning the Biocore Data 
Team), any probesets that interrogate multiple transcripts are set to 
return NA by default. You can change this behavior using the 
toggleProbes() function. I did a quick test of that the other day, and 
it doesn't appear that was done with this package. But you might try 
yourself.

You might also contact the maintainer directly (we don't make these 
packages), to see if he can give more complete answers.

Best,

Jim


>
> Moreover, when using the annotation from oligo (which retrieves NetAffx
> Biological Annotation):
> pData(featureData(OligoEset))["8019631","geneassignment"]
> returns NR_002716
>
> I'm a little bit confused about this.
> Thanks again,
> Javier
>
>
> On 16/04/2011 20:40, James MacDonald wrote:
>> Hi Javier,
>>
>> The annotation of Affy chips tends to change over time, and this might
>> be an instance of that. If you check netaffx for this probeset, the
>> transcript it measures is described as 'multiple', and if you blat the
>> sequence they built the probeset against, it matches all over the place.
>> So it may be that in the past they claimed a direct match and now they
>> don't.
>>
>> You could investigate this further by looking at older versions of the
>> annotation files if you care to know more.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>> James W. MacDonald, M.S.
>> Biostatistician
>> Douglas Lab
>> 5912 Buhl
>> 1241 E. Catherine St.
>> Ann Arbor MI 48109-5618
>> 734-615-7826
>>>>> Javier Pérez Florido 04/16/11 8:16 AM>>>
>> Dear list,
>> I'm trying to get the ENTREZIDs of some Affy_IDs of GeneChip Human Gene
>> ST 1.0 Arrays through hugene10sttranscriptcluster package. Depending on
>> the R version, the results are different.
>> For example, in R 2.12.2:
>> > mget("8104901",hugene10sttranscriptclusterENTREZID)
>> $`8104901`
>> [1] "3575"
>>
>> But
>> >mget("8019631",hugene10sttranscriptclusterENTREZID)
>> Error en .checkKeys(value, Lkeys(x), x at ifnotfound) :
>> value for "8019631" not found
>>
>> The sessionInfo is:
>>
>> sessionInfo()
>> R version 2.12.2 (2011-02-25)
>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252
>> [3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
>> [5] LC_TIME=Spanish_Spain.1252
>>
>> attached base packages:
>> [1] grid tools tcltk stats graphics grDevices utils
>> [8] datasets methods base
>>
>> other attached packages:
>> [1] annotate_1.28.1 oneChannelGUI_1.16.5
>> [3] girafe_1.2.0 genomeIntervals_1.6.0
>> [5] intervals_0.13.3 ShortRead_1.8.2
>> [7] lattice_0.19-17 Rsamtools_1.2.3
>> [9] Biostrings_2.18.4 GenomicRanges_1.2.3
>> [11] baySeq_1.4.0 edgeR_2.0.5
>> [13] IRanges_1.8.9 preprocessCore_1.12.0
>> [15] GOstats_2.16.0 graph_1.28.0
>> [17] Category_2.16.1 tkWidgets_1.28.0
>> [19] DynDoc_1.28.0 widgetTools_1.28.0
>> [21] affylmGUI_1.24.0 affyio_1.18.0
>> [23] affy_1.28.0 limma_3.6.9
>> [25] hugene10sttranscriptcluster.db_6.0.1 org.Hs.eg.db_2.4.6
>> [27] RSQLite_0.9-4 DBI_0.2-5
>> [29] AnnotationDbi_1.12.0 Biobase_2.10.0
>>
>> loaded via a namespace (and not attached):
>> [1] BSgenome_1.18.3 genefilter_1.32.0 GO.db_2.4.5
>> GSEABase_1.12.2
>> [5] hwriter_1.3 RBGL_1.26.0 splines_2.12.2
>> survival_2.36-5
>> [9] XML_3.2-0.2 xtable_1.5-6
>>
>> However, in R 2.10.0
>> mget("8104901",hugene10sttranscriptclusterENTREZID)
>> $`8104901`
>> [1] "3575" (the same as before in R 2.12.2)
>>
>> > mget("8019631",hugene10sttranscriptclusterENTREZID)
>> $`8019631`
>> [1] "6066" (there is no error like in R 2.12.2)
>>
>> The sessionInfo is:
>> R version 2.10.0 (2009-10-26)
>> i386-pc-mingw32
>>
>> locale:
>> [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252
>> [3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
>> [5] LC_TIME=Spanish_Spain.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] limma_3.2.3
>> hugene10sttranscriptcluster.db_4.0.1
>> [3] org.Hs.eg.db_2.3.6 RSQLite_0.9-2
>> [5] DBI_0.2-5 AnnotationDbi_1.8.2
>> [7] Biobase_2.6.1
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.10.0
>>
>> Why this error for Affy_ID 8019631 when R2.12.2 is used?
>> Thanks,
>> Javier
>>
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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