[BioC] Using another array system but affy

[Wolfgang Huber]

Dear Erika,

thank you! The more precise question makes it much easier to give a
useful answer :)

* for normalization, consider quantile normalization (in limma) or vsn
(either through that package directly or via limma)

* for quality assessment, consider the arrayQualityMetrics package
(see http://www.microarray-quality.org/quality_metrics.html - for using
it with one color data, you need to provide them in the form of an
ExpressionSet).

* for differential expression with empirical Bayes, limma.

Best wishes
 Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber



Erika ha scritto:
> Dear Wolfgang,
> 
> My apologies, I'll try to make my question more precise. I've got a table
> with intensity raw data and flag data obtained from 14 codelink arrays, each
> one from a distinct sample, from two categories. I'd like to know how I
> could normalize this data and find differentiatly expressed genes.
> With affy array data, I used to run rma and mas5, and then run empirical
> bayes to find differentiatly expressed genes.
> I hope I made my point clear.
> 
> Best wishes
> 
> Erika
> 
> 2007/11/28, Wolfgang Huber <huber at ebi.ac.uk>:
>> Dear Erika,
>>
>>> I'm a newbie to bioconductor, but I've already done some analysis an
>> affy
>>> arrays. However, I've got some data obtained in the codelink system that
>> I'd
>>> like to analyze in bioconductor as well. What packages should I use? Can
>>> affy packages be used for these data?
>> Please have a look at the limma package.
>>
>> You might also try to formulate your question more precisely. "analyse"
>> is a fairly unspecific task description, almost all of the packages on
>> Bioconductor can be used for some kind of analysis or other.
>>
>> Best wishes
>>    Wolfgang
>>
>> ------------------------------------------------------------------
>> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>>