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: http://svitsrv25.epfl.ch/R-doc/library/exonmap/html/si.html 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 library(exonmap) xmapConnect() # 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", "NB1MoEX1H3.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 empty list. 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? Peter

Hi Peter, 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() or exonmap:::si() 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, Michal -----Mensaje original----- De: bioconductor-bounces at stat.math.ethz.ch en nombre de Peter Saffrey Enviado el: mi? 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: http://svitsrv25.epfl.ch/R-doc/library/exonmap/html/si.html 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 library(exonmap) xmapConnect() # 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", "NB1MoEX1H3.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 empty list. 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? Peter _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor