Entering edit mode
Wolfgang Raffelsberger
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160
@wolfgang-raffelsberger-1805
Last seen 10.3 years ago
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 G?nomique Int?gratives
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