way to normalize copy number data for small RNAs/miRNAs?

[vebaev]

Hi all,
I have searching for a method for normalization if I want to do a diff. expression comparison on 4 datasets from illumina small RNAs(2 controls and 2 samples).
Is there a way to do a normalization and compare them or just to do a copy number comparison and calculate folds?


PS
I have tested several tools for miRNA, but most of them do not provide a way for multiple compareson (maybe only mirTools). In other way what is the obligatory step so the diff. expression of the copy numbers to be accepted in papers?

Thanks

[NicoBxl]

DESeq or edgeR package in R.

you can compare two groups of samples. It take as input a read count matrix (each line for a miRNA and each column for a sample ).

http://www-huber.embl.de/users/anders/DESeq/

http://bioconductor.org/packages/release/bioc/html/edgeR.html

[Claudia34]

You can also have a look on bayseq...

These packages have methods to normalize counts... But you can also use RPKM... Or use your proper normalizator (total counts per instance)