how to set library size in DESeq? i know how to set library size in edgeR d <- DGEList(counts = d, lib.size = c(9893630,11055814,11207084,9663487,11455088,8140053), group = group)#??DGEList?? but donot know how to set library size in DESeq it seems i can set size factor sizeFactors(object) <- value or pData(cds)$sizeFactor <- value but how to set library size? -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

On 02/15/2012 04:24 AM, wang peter wrote: > how to set library size in DESeq? > i know how to set library size in edgeR > d<- DGEList(counts = d, lib.size = > c(9893630,11055814,11207084,9663487,11455088,8140053), group = > group)#??DGEList?? > but donot know how to set library size in DESeq > it seems i can set size factor > > sizeFactors(object)<- value or pData(cds)$sizeFactor<- value > but how to set library size? > The size factor is all there is to set. For the analysis, the algorithm only needs to know the size of a library _relative_ to the other libraries. The total library size is irrelevant. In edgeR, the information is split over two field, one with the library sizes, and one with normalization factors. If you multiply the library sizes with the normalization factors (and divide by some constant to get values close to one), you get edgeR's equivalent to DESeq's size factors, and (to my knowledge) this is all that edgeR uses internally. Why would you want to set the library size? Simon