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Old 08-29-2011, 07:20 AM   #1
Location: Fresno, CA

Join Date: May 2010
Posts: 27
Default microRNA normalization


Does anyone know the reasonable normalization methods for microRNA data analysis?
I already trimmed adaptor, mapped these reads to the reference, and counted the number of reads that mapped on the known microRNA seq.

What I have is a list of known mature microRNAs' ID and sequence, and the number of reads mapped to this miRNAs.
I have 5 samples and want to compare differential expression among them.

How do you normalize the number of mapped reads in order to compare the results from different samples?
Any RPKM-like methods?

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Old 08-29-2011, 08:50 AM   #2
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Location: Plovdiv, Bulgaria

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Use Deseq just with the raw counts and make diff.expr
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Old 08-29-2011, 08:15 PM   #3
Location: Fresno, CA

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Thanks vebaev,
Do you use Deseq for miRNA expression analysis?
One of my concern is the number of miRNA I have in my list is small, 300 ~ 800, depending on a category.
Can I assume that most of miRNA does not change expression levels as we do in mRNA expression analysis?
I think Deseq is good for gene expression analysis, ie. most of genes in some thousands of transcripts do not show expression changes. But I'm not sure miRNA expression analysis adopt this hypothesis.

Last edited by kenosaki; 08-29-2011 at 08:20 PM.
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