[BioC] exonmap error & questions (Affy mouse exon arrays)

[Wolfgang Raffelsberger]

Dear Bioconductors,

I have a few questions concerning the use of the exonmap package for 
(mouse) Affymetrix exon arrays :

Following the instructions from the exonmap-vignette or the "example 
workflow" one typically first creates a vector called 'sigs' containing 
the retained/selected (row)names of rma-processed probe-sets.
If I understand right, the exonmap package uses identifiers different to 
the ones from Affymetrix.  In the case of my mouse data I get for sigs 
something like  "4304922","4304923" etc.
Following the "example workflow" unfortunately I can't get the 
select.probewise() function working (see code below).
Besides, I have difficulty in aligning the results of  exon.details() to 
the original data (see code below).
When using other methods (than pc() ) for identifying differentially 
expressed genes I get stuck at the step of adding/showing my 
test-statistics or original data together with the results from 
exon.details() or gene.details() .

Last point : Is there a way to retreive the corresponding Affymetrix IDs 
? (I guess the QSL tables contain this information: Could this be it the 
table "probeset" ?)

Thanks inadvance for all hints,
Wolfgang


Here the code :

 library(exonmap) ; library(affy)
 xmapDatabase("Mouse")
 dat.raw <- read.exon()
 dat.raw at cdfName <- "mouseexonpmcdf"    
 eset.rma <- rma(dat.raw)
 pc.rma <- pc(eset.rma,"treatment",c("wt","KO"))
 sigs <- names(fc(pc.rma))[abs(fc(pc.rma)) > 1 & tt(pc.rma) < 1e-04]
 sigs[1:2]                   # get: "4304922","4304923" , ...

# problem  with filtering :
 sigs.exonic <-  select.probewise(sigs,filter="exonic")            # 
mt.level :    multi-target score to filter by
# get  :
Error in mysqlExecStatement(conn, statement, ...) :
  RS-DBI driver: (could not run statement: Column 'probeset_id' in field 
list is ambiguous)

# similarly with the command below I get the same error as above ..
 sigs.intronic <-  select.probewise(sigs,filter=c("intronic"))         # 
mt.level :    multi-target score to filter by
# get :
Error in mysqlExecStatement(conn, statement, ...) :
  RS-DBI driver: (could not run statement: Column 'probeset_id' in field 
list is ambiguous)

## now suppose that I selected exons by another method than pc()  and 
that they are in sigs1
sigs1[1:2]          # get : "4304925","4304927", ...

# similarly I run
 sig1.exons <- probeset.to.exon(sigs1)
 sig1.genes <- probeset.to.gene(sigs1)
 sig1.transcr <- probeset.to.transcript(sigs1)
 
# probeset.details(sig.exons)
 gene.details(sig1.genes)   # OK
 exon.details(sig1.exons)   # OK

# the functions used above gives a very nice summary about the gene & 
exon infomation;
# but how can I find out which elements of my initial data they 
represent ? {ie map it to rownames(exps(eset.rma)) }
# I would need this if I wanted to show for example my alternative 
test-statstics or the the intial RMA values as an additonal column ...


 > sessionInfo()
R version 2.7.0 (2008-04-22)
x86_64-unknown-linux-gnu

locale:
C

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

other attached packages:
 [1] limma_2.14.4         exonmap_1.6.02       plier_1.10.0       
 [4] RMySQL_0.6-0         DBI_0.2-4            RColorBrewer_1.0-2 
 [7] simpleaffy_2.14.05   gcrma_2.12.1         matchprobes_1.12.0 
[10] genefilter_1.20.0    survival_2.34-1      affy_1.16.0        
[13] preprocessCore_1.0.0 affyio_1.6.1         Biobase_2.0.1      

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.0.6 RSQLite_0.6-8       annotate_1.18.0   



 
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et Génomique Intégratives
CNRS UMR7104, IGBMC 
1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
Tel (+33) 388 65 3300         Fax (+33) 388 65 3276
http://www-bio3d-igbmc.u-strasbg.fr/~wraff
wolfgang.raffelsberger at igbmc.fr