[BioC] exonmap/xmapcore and splicing.index
michal.okoniewski at fgcz.ethz.ch
Wed Sep 29 19:01:39 CEST 2010
A quick hack that I use at the moment is using both libraries,
do xmapConnect() for exonmap and xmap.connect() for xmapcore
and calling explicitely the functions like: xmapcore:::probe.to.hit()
As I understand from what the guys from PICR in Manchester are doing
it is a transition period after database format change and hope that
it will be sorted out soon.
all the best,
De: bioconductor-bounces at stat.math.ethz.ch en nombre de Peter Saffrey
Enviado el: mié 29/09/2010 13:19
Para: bioconductor at stat.math.ethz.ch
Asunto: [BioC] exonmap/xmapcore and splicing.index
I am analysing Affymetrix mouse exon arrays (MoEx-1_0) using xmapcore
and would like to use the splicing index function to compare the levels
of splicing in two conditions. It's documented here:
Unfortunately, this function is only available in exonmap, the (now
deprecated) version of xmapcore. I have managed to install exonmap but I
get errors calling si. Here is what I do:
# start exonmap and connect to db
# read array data and compute rma
adata <- read.exon()
adata at cdfName <- "mouseexonpmcdf"
x.rma <- rma(adata)
# setup the appropriate columns for the two conditions
gps <- list(c("KC4MoEX1E141.CEL", "KC4MoEX1E142.CEL",
"KC4MoEX1E143.CEL"), c("NB1MoEX1H1.CEL", "NB1MoEX1H2.CEL",
# call splicing index algorithm
mysi <- si(x.rma, c("ENSMUSG00000000001", "ENSMUSG00000000003"), gps=gps)
and the error:
Error in fix.by(by.y, y) : 'by' must specify valid column(s)
In addition: Warning message:
In is.na(cols) : is.na() applied to non-(list or vector) of type 'NULL'
Stepping down through the functions it's calling, it looks like a
problem in gene.to.exon.probeset, which is not working and returning an
I thought about trying to port this function to xmapcore, but I'm not
very experienced in R and I don't even know how to get at the source for
the modules I've downloaded.
Is anybody using xmapcore/exonmap to do alternative splicing analysis?
Can they provide me with any pointers or alternative tools?
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