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Hi, You can P-values and Q-values as below: sam_p_values <- as.matrix(samoutput at p.value[myDEGenes]); sam_q_values <- as.matrix(samoutput at q.value[myDEGenes]); Replace myDEGenes with character set of All Genes and you can get output of all p-values or q-values of the genes or probeIDs. Saurin Quoting Assa Yeroslaviz <frymor at="" gmail.com="">: > Hi, > > i've got a problem extracting the p values of my significance genes. > I did a sam analysis and want to see the p values of all of the genes and > only of the sig. genes. > I did > >> samresult at p.value > to get all my p values. > > but I just can't get the command to extract only the p values of my sig. > genes. > > first try was : >> samresult at mat.sig$p.value > NULL > > second try: >> samresult at mat.sig[,"p.value"] > Fehler in "[.data.frame"(samList at mat.sig, , "p.value") : > nicht definierte Spalten gew?hlt > > It seems i just can't connect the mat.sig and the p.values columns of my > data. > > I would like to have a table/ matrix with the names of the genes and the > pvalues of this genes. If it is possible I would also like to have the FDR > of this list. > > I would be very happy to get some help here. > > THX > > > Assa > -- > Assa Yeroslaviz > Loetzener Str. 15 > 51373 Leverkusen > > [[alternative HTML version deleted]] > >

Hi Assa, when sam.out is the output of sam(...), then > sam.out at p.value respectively > sam.out at q.value will do the trick. Best, Holger > --- Urspr?ngliche Nachricht --- > Von: "Assa Yeroslaviz" <frymor at="" gmail.com=""> > An: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Betreff: [BioC] p values of significant genes in SAM > Datum: Mon, 6 Mar 2006 15:22:15 +0100 > > Hi, > > i've got a problem extracting the p values of my significance genes. > I did a sam analysis and want to see the p values of all of the genes and > only of the sig. genes. > I did > > >samresult at p.value > to get all my p values. > > but I just can't get the command to extract only the p values of my sig. > genes. > > first try was : > > samresult at mat.sig$p.value > NULL > > second try: > >samresult at mat.sig[,"p.value"] > Fehler in "[.data.frame"(samList at mat.sig, , "p.value") : > nicht definierte Spalten gew?hlt > > It seems i just can't connect the mat.sig and the p.values columns of my > data. > > I would like to have a table/ matrix with the names of the genes and the > pvalues of this genes. If it is possible I would also like to have the FDR > of this list. > > I would be very happy to get some help here. > > THX > > > Assa > -- > Assa Yeroslaviz > Loetzener Str. 15 > 51373 Leverkusen > > [[alternative HTML version deleted]] > > -- Echte DSL-Flatrate dauerhaft f?r 0,- Euro*!