Thank you. That worked fine for me. On Sat, Jul 13, 2013 at 2:40 AM, Sylvain Brohée <sbrohee@ulb.ac.be> wrote: > Hi, > > You should maybe try something like > > mat=read.delim(file="exp_mat.**txt", header=T, row.names = 1) > > Cheers, > > Sylvain > > Le 13/07/2013 04:14, Chirag Gupta a écrit : > > 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! >> >> >> >> > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > -- *Chirag Gupta* Department of Crop, Soil, and Environmental Sciences, 115 Plant Sciences Building, Fayetteville, Arkansas 72701 [[alternative HTML version deleted]]