Question About Use Of Samr

Question

[Layla]

Hi: I have the following table in csv format in Excel:

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

[Neilfws]

It would help to know (1) which organism and (2) what is the source of these gene IDs/names - are they Entrez Gene IDs, for example? Then we can address the topic of ID conversion.

Answer 1

[Sukhi Singh]

I tried this, when you convert the data.frame to matrix it should ideally convert it as a character matrix but it converts to numerics, so your first column which contains the gene names are also converted to numeric. Try typeof(t[,1]) and I am sure its not character. So, the problem is not with package but with the data transformation. Also, try as.numeric(m[,1]) to get the gene names converted to numeric form and see if they match the Gene Names in the samfit object. Then, you can use %in% to check which gene names corresponds to what. I am not able to think of a simple solution yet.