[BioC] Affymetrix genechip miRNA array analysis

[Mark Cowley]

Hi,
you can download the CDF from Affymetrix, so you *should* be able to  
run a simple affy and limma analysis;
however there are lots of different species on this chip, so you may  
want to subset probes to the relevant ones for your species prior to  
the limma analysis
(my version of the affy miRNAQCtool keeps crashing, so I can't use it  
to normalise even the example files downloaded from Affy)

cheers,
Mark
-----------------------------------------------------
Mark Cowley, PhD

Peter Wills Bioinformatics Centre
Garvan Institute of Medical Research, Sydney, Australia
-----------------------------------------------------

On 08/10/2009, at 6:01 AM, cstrato wrote:

> 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  		 	   		   
>> _________________________________________________________________
>> Chatea sin límites en Messenger con la tarifa plana de Orange
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor