Hi

I have a gene expression matrix of 21746 X 16 in a .txt file
This is a subset shown below

   Locus ID Stage1 Stage2 Stage3 Stage4  AT1G01010 5.249586 4.966158765
5.523153 5.872942491  AT1G01030 4.645518 4.13401959 4.480153 4.278106108
AT1G01040 8.367959 9.004792207 7.045742 7.969386196  AT1G01050 10.05919
9.937913426 9.822789 9.761852365  AT1G01060 9.32046 7.729952133 7.450211
9.509721634  AT1G01070 4.967583 3.901125815 6.429503 6.114024786  AT1G01080
7.176741 6.428628132 8.923322 7.39688902  AT1G01090 10.38129 9.557772838
10.99624 10.11981964  AT1G01100 12.12936 12.43516812 11.67846 10.92524171
I want to read in this text file and calculate pearson correlations between
gene pairs across the samples.

I tried this

>mat=read.table(file="exp_mat.txt", header=T, sep="\t")

but when I do rownames(exp.mat), it shows numbers from to the total rows.

Which is the correct method to read in such a file so that the rows and
columns are preserved and cor() can be run on rows?

Thanks!



-- 
*Chirag Gupta*
Department of Crop, Soil, and Environmental Sciences,
115 Plant Sciences Building, Fayetteville, Arkansas 72701

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