RNA seq normalization(TMM)

Question

[maryak]

i have htseq-count data now i want to normalize it using TMM for diffrential expression analysis .can anybody tell me how to do this Thanking in anticipation

Answer 1

[h.mon]

The edgeR User Guide is an excellent read, and has the answer to this question, and probably the answer to some questions you will have in the near future.

[maryak]

can you please guide me in the form of code because i am new with R

[h.mon]

Read the edgeR User Guide, it has plenty of code examples to guide you through the whole analysis, from the very beginning to the very end. Then, if /when you have difficulties, show us how is your data (ideally, with a small example), tell us what you did (the code), and the error you got.

The Similar Posts links to the right are also a great resource, and indeed I found one link with code and explanations about TMM normalization which would probably be very helpful to you.

[maryak]

i have run this code but no file is created even after the program is executed successfully and no error message appears

library(edgeR)
seqdata <- read.delim("C:\\Users\\hp folio\\Desktop\\TCGA-DLBC.htseq_counts.tsv")
scale.factors <- calcNormFactors(seqdata,lib.size=NULL method = "TMM")
norm.data <- t(t(seqdata)/(scale.factors*lib.size))
write.csv(norm.data,"C:\\Users\\hp folio\\Desktop\\TMM.csv")

[k.kathirvel93]

I suspect that you have a problem on write.csv line. Check your path is correct or not.

[maryak]

if path is incorrect at least it must show some error... and i checked there is no problem in path

[maryak]

if path is incorrect at least it must show some error... and i checked there is no problem in path