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

vebaev · 03-26-2011, 01:44 AM

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 · 03-28-2011, 12:23 AM

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/rel...tml/edgeR.html

Claudia34 · 03-28-2011, 03:18 AM

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)

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03-26-2011, 01:44 AM	#1
vebaev Senior Res. Location: Plovdiv, Bulgaria Join Date: Oct 2008 Posts: 110	way to normalize copy number data for small RNAs/miRNAs? 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

03-28-2011, 12:23 AM	#2
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	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/rel...tml/edgeR.html

03-28-2011, 03:18 AM	#3
Claudia34 Junior Member Location: Geneva, Switzerland Join Date: Sep 2010 Posts: 9	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)