[BioC] Affymetrix genechip miRNA array analysis

[cstrato]

Dear Jordi,

Until now I did not receive any feedback to my mail.
Please note that rma does only use PM probes, so the missing mismatch 
probes do not matter.
Furthermore, the manual for the Affymetrix "miRNA QC Tool" mentions that 
you can set the tool to use rma, however, I could not test it, since the 
version that I have downloaded is missing the "Save" button for this 
purpose which is shown in the corresponding figure of the manual. You 
can download the tool from:
http://www.affymetrix.com/partners_programs/programs/developer/tools/devnettools.affx#1_1
Personally, I do not have any experience with miRNA and have only access 
to the three CEL-files which you can download from Affymetrix. Thus, I 
am afraid that I cannot give you any helpful suggestions.

Best regards
Christian

Jordi Altirriba wrote:
> 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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