Hi everybody, I am relatively new to R, so this might be a stupid question. I am actually working with edgeR and I'd like to extract a file with the normalized expression values. I do have the normalization factors in the DGEList and the raw values, but I cannot find (or write, it's to early for that because of my scarce knowledge) a function to extract the normalized ones. Would be nice if somebody could help me with that. Thanks in advance, Philipp

Hi Philipp For normalised counts on the log2 scale do: effective.lib.size <- d$samples$lib.size * d$samples$norm.factors y <- log2( t(t(d$counts+0.5) / (effective.lib.size+0.5)) ) Best iain ----- Original Message ----- From: Philipp Brand <philipp.brand@uni-duesseldorf.de> To: bioconductor at r-project.org Cc: Sent: Friday, 16 March 2012, 12:22 Subject: [BioC] edgeR-How to obtain a list of normalized expression values Hi everybody, I am relatively new to R, so this might be a stupid question. I am actually working with edgeR and I'd like to extract a file with the normalized expression values. I do have the normalization factors in the DGEList and the raw values, but I cannot find (or write, it's to early for that because of my scarce knowledge) a function to extract the normalized ones. Would be nice if somebody could help me with that. Thanks in advance, Philipp _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor