small RNA DE analysis

[NicoBxl]

Hi,

I've sequenced (Illumina GA II) 6 leukemic samples and a sample composed of a pool of 3 control. The purpose of the work is the analysis of the miRNAome and the up/down regulated miRNA.

For the DE analysis, I use the DESeq package.

So I've a matrix where each colum is a sample and each line a miRNA.
Since my control is a pool of 3 control sample, can I use three same columns for the control. Example :

Three same columns

	leu1	leu2	leu3	ctrl	ctrl'	ctrl''
miR-1     x       y       z      a       a       a
miR-2     x'      y'      z'     a'      a'      a'
.
.

or

One colum for the pool of 3 ctrl

	leu1	leu2	leu3	ctrl
miR-1     x       y       z      a      
miR-2     x'      y'      z'     a'     
.
.

Anyone can help me ?

Thanks,

N.

[NicoBxl]

nobody knows ?

[Simon Anders]

As you have only one control sample (even though it is pooled), it should get only one column. Your design is not ideal and without some fiddling this may cost you some power, but it should work that way.