[BioC] SQLForge and probes that map to multiple genes

Cei Abreu-Goodger cei at sanger.ac.uk
Mon Jul 14 17:20:51 CEST 2008

Hi all,

I'm trying to generate an annotation package for a custom mouse Affy 
chip (GNF1M). I'm a bit confused about how the package deals with probes 
that are mapped to multiple genes. Sure, when I have a single column of 
identifiers everything works nicely, but what exactly happens when I 
have more than one gene per probe?

I tried a mock annotation, code below:

# Running code to build the annotation package
 > library(AnnotationDbi)
 > library(mouse.db0)
 > refseqs <- "gnf1m.test.tab"
 > read.table(refseqs)
               V1        V2        V3
1   gnf1m00050_at NM_008929 NM_172283
2 gnf1m00051_a_at NM_007487 NM_172283
3 gnf1m00052_a_at NM_178939 NM_172283
4 gnf1m00053_a_at NM_181666 NM_172283
5 gnf1m00054_a_at NM_026430 NM_172283
6 gnf1m00055_a_at NM_029916 NM_172283
7 gnf1m00056_a_at NM_181666 NM_172283
 > makeMOUSECHIP_DB(affy=FALSE, prefix="test", fileName=refseqs, 
+                  outputDir=".", version="0.9", 
manufacturer="GNF-Affymetrix", chipName="gnf1m")

After installing, though, it seems to me that I have something strange. 
Although I added the refseq "NM_172283" to all of the probes, in the 
annotation it only went to two of them, the last one and another that 
was identical (see below). This might not be the best example, but if I 
do have probes that map to different genes, what's the best way of 
making SQLForge aware of this?



# loading and accessing the annotation package
 > library(test.db)
 > as.list(testREFSEQ)
[1] "NM_008929" "NP_032955"

[1] "NM_001039515" "NM_007487"    "NP_001034604" "NP_031513"  

[1] "NM_178939" "NP_849270"

[1] "NM_172283" "NM_181666" "NP_758487" "NP_858052"

[1] "NM_026430" "NP_080706"

[1] "NM_029916" "NP_084192"

[1] "NM_172283" "NM_181666" "NP_758487" "NP_858052"

 > sessionInfo()
R version 2.7.0 (2008-04-22)


attached base packages:
[1] stats     graphics  grDevices datasets  tools     utils     methods 
[8] base    

other attached packages:
[1] test.db_0.9         mouse.db0_2.1.4     AnnotationDbi_1.2.0
[4] RSQLite_0.6-8       DBI_0.2-4           Biobase_2.0.0     

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