Question: samr package problems significant genes
0
gravatar for Assa Yeroslaviz
9.7 years ago by
Assa Yeroslaviz1.4k
Munich, Germany
Assa Yeroslaviz1.4k wrote:
-- Hi everyone, I'm Doing a samr analysis of Arabidopsis genes with the R package samr. This is the script I'm using: library(impute) library(samr) drought <- read.table("drought_stress_1. 0.txt",header=TRUE, sep="\t", quote="",row.names=1)# einlesen der Daten TS_vector=paste(c(rep(1,24),rep(2,24)),"Time",rep(c(1,3,6,9,24,48),2), sep="") start=c(1,7,13,19, 25, 31, 37, 43) for(i in start){ TS_vector[i]=paste(TS_vector[i],"Start",sep="")} for(i in start+5){TS_vector[i]=paste(TS_vector[i],"End",sep="")} TS_group <- cbind( drought[,1],drought[,9],drought[,17],drought[,21],drought[,7],drought[ ,13],drought[,25],drought[,34],drought[,41],drought[,45],drought[,29], drought[,37], drought[,2],drought[,10],drought[,18],drought[,22],drought[,8],drought [,14],drought[,26],drought[,35],drought[,42],drought[,46],drought[,30] ,drought[,38], drought[,3],drought[,11],drought[,19],drought[,23],drought[,9],drought [,15],drought[,27],drought[,36],drought[,43],drought[,47],drought[,31] ,drought[,39], drought[,4],drought[,12],drought[,20],drought[,24],drought[,10],drough t[,16],drought[,28],drought[,37],drought[,44],drought[,48],drought[,32 ],drought[,40] ) gene_names <- row.names(drought) drought_samr=list(x=TS_group, y=TS_vector, logged2=TRUE) samr.obj.slope<- samr(drought_samr, resp.type="Two class unpaired timecourse", nperms=100, time.summary.type="slope") delta.table.slope <- samr.compute.delta.table(samr.obj.slope) delta.table.slope # choose delta value according to Parameters ("# med falsepos" should be under 1.0) samr.plot(samr.obj.slope, 0.8868236899) siggenes.table <- samr.compute.siggenes.table(samr.obj.slope, 0.8868236899, drought_samr, delta.table.slope) But unfortunately, Im not getting anywhere. I can do the analysis with 100 permutations, I than try to make a list of the significant genes, but I'm getting this error message: > siggenes.table <- samr.compute.siggenes.table(samr.obj.slope, 0.8868236899, drought_samr, delta.table.slope) Error in dimnames(res.up) = temp.names : length of 'dimnames' [2] not equal to array extent I would be greatful to anyone who can help me solving this dimensional problem. THX Assa Yeroslaviz Assa Yeroslaviz Kockelsberg 22 51371 Leverkusen Sent from Dusseldorf, NW, Germany [[alternative HTML version deleted]]
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ADD COMMENTlink modified 9.7 years ago by Elana Fertig10 • written 9.7 years ago by Assa Yeroslaviz1.4k
Answer: samr package problems significant genes
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gravatar for Elana Fertig
9.7 years ago by
Elana Fertig10
United States
Elana Fertig10 wrote:
Assa Yeroslaviz <frymor at="" ...=""> writes: > Assa, I'm not sure if you found the solution to this yet, but I just was able to get rid of that same error by adding in a list of bothe genenames and geneid in the data to samr. So, d=list(x=x, y=y, geneid=geneid, genenames=genenames, logged2 = TRUE) Cheers, Elana
ADD COMMENTlink written 9.7 years ago by Elana Fertig10
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