[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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