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

Julian Lee julian at omniarray.com
Mon Nov 3 05:22:51 CET 2008


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


-- 
Julian Lee
Bioinformatics Specialist
Cellular and Molecular Research
National Cancer Center Singapore



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