[BioC] question about samR and Excel
Juan Gutierrez
wits.gutierrez at gmail.com
Wed Nov 21 23:23:12 CET 2012
I have the following table in csv format in Excel:
1 1 1 2 2 2
1415670_at 1 365.1 293.4 288.9 394.5 312 381.6
1415671_at 2 556.1 584.2 567.8 592.8 471.6 513.1
1415672_at 3 1048.3 763.1 1074.9 852.3 826.1 898.3
1415673_at 4 60.8 51.7 51.6 224 248.4 150.7
1415674_at 5 129.1 107.2 230.4 175.5 250.5 172.4
I have been using SAM for getting a list of up and down regulated
genes. For that purpose there is an Excel plugin that does the task
with the above mentioned file.
The problem that I have is that I need to use R for analizing this
data, for that there is a package called SAMR. I want to get the list
of up and down regulated genes with the names that are in the first
column, but no success at all.
The manual is available here:
http://cran.r-project.org/web/packages/samr/samr.pdf
The small program that I made was:
filename<-"test.csv"
y<-c(1,1,1,2,2,2) //I have to do this in this way, but I
will extract the
//first row from the csv file later
m<-read.csv(filename,sep=",",row.names=1)
t<-as.matrix(m)
samfit<-SAM(t,y,resp.type="Two class unpaired")
when I put
print(samfit)
I got the following data:
Genes down
Gene ID Gene Name Score(d) Numerator(r) Denominator(s+s0) Fold Change
[1,] g1753 1753 -2.025 -707.725 349.446 0.582
[2,] g1375 1375 -1.038 -272.583 262.7 0.797
[3,] g1302 1302 -0.955 -296.733 310.685 0.739
[4,] g1598 1598 -0.923 -352.725 382.068 0.722
[5,] g1500 1500 -0.913 -442.142 484.177 0.352
but I need the gene names and not that gene ID in the list of genes up
and genes down
any help?
Thanks
J M
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