-- 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],drought[,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

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