Hello, I have three sequenced (Illumina) genomic libraries (L1,L2,L3) and three biological replicates for each (A,B,C). I'd like to compare those libraries, and find which are the most similar (e.g. is "L1" more similar to "L2" or to "L3", based on the profile of mapped short reads in the libraries). I've generated windows of 2kb over the genome, and counted how many reads from each library/replicate fall within the window. The result is similar to this: --- Window L1_RepA L1_RepB L1_RepC L2_RepA L2_RepB L2_RepC L3_RepA L3_RepB L3_RepC chr1_1 10 15 0 1000 1100 800 90 0 300 chr1_2 77 80 99 3 4 12 100 200 193 ... (and so forth for every window over the chromosomes). --- What would be a reliable way to compare these three libraries, as a whole (meaning, not just "differential expression" on each window independently, as would be done with genes) ? Thank you, -gordon -- output of sessionInfo(): . -- Sent via the guest posting facility at bioconductor.org.

Sounds like a job for edgeR's plotMDS function (which also invisibly returns the MDS object). On Sun Nov 24 04:59:38 2013, Gordon [guest] wrote: > > Hello, > > I have three sequenced (Illumina) genomic libraries (L1,L2,L3) and three biological replicates for each (A,B,C). > I'd like to compare those libraries, and find which are the most similar (e.g. is "L1" more similar to "L2" or to "L3", based on the profile of mapped short reads in the libraries). > > > I've generated windows of 2kb over the genome, and counted how many reads from each library/replicate fall within the window. > > The result is similar to this: > --- > Window L1_RepA L1_RepB L1_RepC L2_RepA L2_RepB L2_RepC L3_RepA L3_RepB L3_RepC > chr1_1 10 15 0 1000 1100 800 90 0 300 > chr1_2 77 80 99 3 4 12 100 200 193 > ... > (and so forth for every window over the chromosomes). > --- > > What would be a reliable way to compare these three libraries, as a whole (meaning, not just "differential expression" on each window independently, as would be done with genes) ? > > Thank you, > -gordon > > > -- output of sessionInfo(): > > . > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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