[BioC] BMP4 probe '1940386' missing in illuminaHumanv2BeadID.db (as compared to illuminaHumanv2ProbeID.db)

Marc Carlson mcarlson at fhcrc.org
Mon Nov 3 20:09:03 CET 2008


Hi Lynn,

Thanks for clarifying this!  The people who are now directly responsible
for this package are Matt Ritchie and Mark Dunning.  I am going to CC
them into this thread so that they can hopefully clarify for us what is
happening with his package. 


  Marc





Lynn Amon wrote:
> Julian,
> I no longer maintain the Illumina annotation packages but I can tell you
> that I made the illuminaHumanv2ProbeID.db package using annotation
> provided by Nuno Barbosa-Morais who BLASTed the probe sequences against
> hg18.  I only used probes which had 100% similarity with refseq
> sequences.  You can find the BLAST results at:
> http://www.compbio.group.cam.ac.uk/Resources/Annotation/
>
> >From what I can see by BLASTing the three probe sequences again against
> the current build, all three have perfect matches with refseq sequences
> for BMP4
> 1940386    AGTAGAGGGATGTGGGTGCCGCTGAGATCAGGCAGTCCTTGAGGATAGAC  
> NM_130851.2, NM_138050.2, NM_001202.3
> 3360703    GAGACGCAGACGCAGAGGTCGAGCGCAGGCCGAAAGCTGTTCACCGTTTT  NM_130851.2
> 1850561    ACGCCGCTGCTGCTCCGGCTGAGTATCTAGCTTGTCTCCCCGATGGGATT   NM_001202.3
>
> Also, all three probes are listed with in the last available
> Illumina-provided annotation file that I can find: 
> HumanWG-6_V2_0_R2_11223189_A
> 1940386    NM_130851.1
> 3360703    NM_130851.1
> 1850561    NM_001202.2
>
> So, I'm a little confused as to why 1940386 is not showing BMP4 as the
> symbol name in the new annotation package.  What are the other
> annotation results for this probe?  RefSeq? Accession?
>
> Marc, do you know what annotation file was used for these packages?
>
> Lynn Amon
>
>
>
> Marc Carlson wrote:
>   
>> Hi Julian,
>>
>> We are not responsible for the mappings used to tie the illumina IDs
>> onto the gene IDs, for those you probably need to talk to the
>> manufacturers.  When we build a new package, all we do is connect those
>> manufacturer provided mappings to the data from public repositories.  If
>> the manufacturer changes their mind about how one of those probes should
>> map we have little choice but to believe them.  But without even seeing
>> these new manufacturer mappings, I would guess that there is probably
>> nothing wrong with this package.  It is (unfortunately) fairly common
>> for manufacturers of microarrays to decide that a probe does not really
>> measure what they originally thought it measured.  This is part of why
>> we rebuild all these packages every six months.  We are trying our best
>> to give you the most current/accurate picture possible. 
>>
>> If you have doubts about the correct mapping of that probe, then please
>> check with the manufacturer to see what they claim their platform
>> measures.  If there are any discrepancies in the package from this, then
>> please let me know immediately.
>>
>>
>>   Marc
>>
>>
>>
>>
>> Julian Lee wrote:
>>   
>>     
>>> Hi,
>>>
>>> may i know the differences between the 2 packages and why is this so. I have a gene of interest on the Illumina platform and have been using the IlluminaHumanv2ProbeID.db package to annotate it, but things have changed when i moved to R.2.8.0 on illuminaHumanv2BeadID.db package.
>>>
>>> I'll illustrate it by an example
>>>
>>> Gene of interest - BMP4
>>>
>>> R.2.7.1
>>> illuminaHumanv2ProbeID.db package
>>>
>>>   
>>>     
>>>       
>>>> bmp4_p<-as.character(unlist(mget('BMP4',revmap(illuminaHumanv2ProbeIDSYMBOL))))
>>>> bmp4_p
>>>>     
>>>>       
>>>>         
>>> [1] "1850561" "1940386" "3360703"
>>>
>>>   
>>>     
>>>       
>>>> sessionInfo()
>>>>     
>>>>       
>>>>         
>>> R version 2.7.1 (2008-06-23) 
>>> i386-pc-mingw32 
>>>
>>> locale:
>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] tools     stats     graphics  grDevices utils     datasets  methods  
>>> [8] base     
>>>
>>> other attached packages:
>>> [1] illuminaHumanv2ProbeID.db_1.1.1 AnnotationDbi_1.2.2            
>>> [3] RSQLite_0.6-9                   DBI_0.2-4      
>>>
>>> All looks well. However, when i upgraded to R.2.8.0, and installed the illuminaHumanv2BeadID.db package, i encountered these results
>>>
>>> R.2.8.0
>>> illuminaHumanv2BeadID.db package
>>>
>>>   
>>>     
>>>       
>>>> bmp4_p<-as.character(unlist(mget('BMP4',revmap(illuminaHumanv2BeadIDSYMBOL))))
>>>> bmp4_p
>>>>     
>>>>       
>>>>         
>>> [1] "1850561" "3360703"
>>>
>>>   
>>>     
>>>       
>>>> sessionInfo()
>>>>     
>>>>       
>>>>         
>>> R version 2.8.0 (2008-10-20) 
>>> i386-pc-mingw32 
>>>
>>> locale:
>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] tools     stats     graphics  grDevices utils     datasets  methods  
>>> [8] base     
>>>
>>> other attached packages:
>>> [1] illuminaHumanv2BeadID.db_1.1.2 RSQLite_0.7-1                 
>>> [3] DBI_0.2-4                      AnnotationDbi_1.4.0           
>>> [5] Biobase_2.2.0 
>>>
>>>
>>> The probeID/beadID "1940386" has disappeared. Why is this so? is there a mistake in the illuminaHumanv2BeadID package? 
>>> Is it possible to achieve reproducible results by upgrading to 2.8.0?
>>>
>>> many thanks
>>>
>>> julian
>>>
>>>
>>>
>>>     
>>>       
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>>   
>>     
>
>
>



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