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

[Marc Carlson]

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
>
>
>