problem with function to interrogate x:Map (exonmap)
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@wolfgang-raffelsberger-1805
Last seen 8.4 years ago
Dear list, following the instructions in the help-pages (exonmap.pdf) I get to a list of 'significant' exons/genes (sigs) but when interrogating xMap (which we have installed locally with the most recent version of mySQL) the query-functions always return empty vectors. After looking more carefully the SQL tables we realized that by furnishing "Probeset ID" from Affymetrix gives correct results. However, the function "names" used with "names(fc(pc.exonmap))[.." returns different identifiers and the corresponding Affymetrix "Probeset ID" are/would not be known at this stage of the analysis ! We realized that the table "probset.sql" allows to retreive such Affymetrix "Probeset ID" (given the names in sigs were mapped with the rownames of the expression-set). But I don't see one of the functions of the package exonmap allowing to do such a query, am I incorrect ?. Using the command, "featureNames" (following the example form "exonmap.example.pdf") we get the same result as with "names(fc(pc.exonmap))[.." , still an output in format that doesn't seem to be the correct one to the correct one for entering the pre-built SQL queries. Any suggestions ? Thank's in advance, Wolfgang Raffelsberger > data(exonmap) > pc.exonmap <- pc(x.rma, "group", c("a", "b")) > sigs <- names(fc(pc.exonmap))[abs(fc(pc.exonmap)) > 1 & tt(pc.exonmap) < 1e-04] > length(sigs) # ger 31 entries > sigs[1:3] # look at the 1st 3 of them ... [1] "3102398" "3102391" "3102439" > > xmapDatabase("Human") # Switching to human database Switching to human database... done. > sig.exons <- probeset.to.exon(sigs) > length(sig.exons) # get NULL > probeset.to.transcript(sigs) # get NULL > select.probewise(sigs, filter = "exonic") # get NULL > > sigs <- c("3743907","3743908") # here I enter some "Probeset ID" from Affymetrix (!) for p53 > probeset.to.transcript(sigs) # get correct result (but in normal case I won't know these IDs !) > probeset.to.exon(sigs) # again OK > > sessionInfo() R version 2.5.1 (2007-06-27) x86_64-unknown-linux-gnu locale: C attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: exonmap plier RMySQL DBI RColorBrewer simpleaffy "1.0.07" "1.6.0" "0.6-0" "0.2-3" "1.0-1" "2.10.31" genefilter survival affy affyio Biobase "1.14.1" "2.32" "1.14.2" "1.4.1" "1.14.1" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique et G?nomique Int?gratives IGBMC 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 wolfgang.raffelsberger at igbmc.u-strasbg.fr
Survival genefilter affy plier affyio exonmap Survival genefilter affy plier affyio • 742 views
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