[BioC] Affymetrix genechip miRNA array analysis

Jordi Altirriba altirriba at hotmail.com
Wed Oct 7 01:29:32 CEST 2009

Sorry for the previous mail in not plain text.
Here is in plain text:

Dear Biocoductor users,
I would like to analyse the presence of some microRNA in a tissue under different conditions.
I am thinking on using the Affymetrix GeneChip miRNA array (launched on March 2009), as our institution has an Affymetrix platform (suggestions from other platforms are welcomed).
I was wondering how to proceed after the hybridization. In other words, can I proceed as a gene expression array (mRNA)? (rma -> limma,  for example) Or are there other specific methods in order to normalize the data, to observe its quality and to get differential expression? 
The miRNA arrays are different from gene expression arrays as there are 4 identical probes for each miRNA and 11 probes for sno/scaRNA. Moreover, there aren’t mismatch probes.
I have just read that Christian Stratowa proposed the use of rma (http://article.gmane.org/gmane.science.biology.informatics.conductor/24682/match=mirna), but at this moment I don’t have found that anybody has given positive or negative feedback to his mail.

Many thanks for your help and suggestions.
Jordi Altirriba
Hospital Clinic
Barcelona, Spain  		 	   		  
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