issues with samR in R

Question

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

dput(m) shows the following info:

structure(list(X.1 = 1:5, X1 = c(365.1, 556.1, 1048.3, 60.8, 129.1), X1.1 = c(293.4, 584.2, 763.1, 51.7, 107.2), X1.2 = c(288.9, 567.8, 1074.9, 51.6, 230.4), X2 = c(394.5, 592.8, 852.3, 224, 175.5), X2.1 = c(312, 471.6, 826.1, 248.4, 250.5), X2.2 = c(381.6, 513.1, 898.3, 150.7, 172.4)), .Names = c("X.1", "X1", "X1.1", "X1.2", "X2", "X2.1", "X2.2"), class = "data.frame", row.names = c("1415670_at", "1415671_at", "1415672_at", "1415673_at", "1415674_a_at"))

Answer 1

'With that small dataset the 'Genes down matrix is NULL but this shows how to get the names of the 'Genes Up' matrix:

> rownames(m)[ as.numeric( samfit$siggenes.table$genes.up[ , "Gene Name"]) ]
[1] "1415674_a_at" "1415673_at"   "1415672_at"  

You need to use what was in the dataframe as a name (a series of numbers) to refer back to the rownames. For your full model fit you should get what you want with:

rownames(m)[ as.numeric( samfit$siggenes.table$genes.lo[ , "Gene Name"]) ]

For future investigation this was discoverable by looking first at the class of 'samfit' and then for a function named: print.SAMoutput and modifying the relevant code No need to use getAnywhere or ::: since the function is not hidden.