[BioC] GEOquery, GSE, and MAList

[James F. Reid]

Hi Timothy,

you can run limma for differential expression analysis on your object 
'gse' which is a list of ExpressionSets, which contains one single 
element because the dataset is not too large. This contains normalized 
log2 ratios after pre-processing done by the authors.
If you want to do quality control and/or apply your own pre-processing 
you can because the authors of this particular GSE have also provided 
the raw data (scanner output txt files). To download these files you can 
use the GEOquery function getGEOSuppFiles. After the download has 
completed you will need to import the data using functions provided in 
limma, see Section 4 in the limmaUsersGuide().

HTH,
James.

On 05/19/2010 01:13 PM, Timothy Wu wrote:
> Hi,
>
> Is it possible to convert GSE obtained using getGEO() into an MAList?
>
> I tried
>
>> gse = getGEO("GSE17308")
>> ma = GDS2MA(gse)
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function "Meta", for signature
> "list"
>
> GSE is not the same as GDS, so it's not surprising that it isn't working.
> However, I don't understand how GSE should be different from GDS to arrive
> to the same data structure. What I ultimately want is to able to connect to
> limma analysis, which in the examples uses an MAList. Any help would be
> appreciated, thank you. :)
>
> Timothy
>
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>
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