[BioC] transfering Illumina Beadarray data from Partek into Bioconductor's beadarray in order to run Limma

[Wei Shi]

Hi Gustavo:

	It seems your data is not the raw data outputted from BeadStudio. I would suggest you follow the case study in limma user guide using your raw data. The case study used a quantile normalization.

Cheers,
Wei

On Mar 16, 2011, at 9:55 PM, Mark Dunning wrote:

> Hi Gustavo,
> 
> The limma package is actually capable of reading and preprocessing
> Illumina data itself. There is an example of this in the Limma user's
> guide, which you can access by typing limmaUsersGuide() in R. The
> function to read Illumina output is called read.ilmn. Personally I
> would take this route rather than going through Partek, as limma also
> has other preprocessing options that are beneficial to the analysis of
> Illumina data.
> 
> Best wishes,
> 
> Mark
> 
> On Tue, Mar 15, 2011 at 8:56 PM, Gustavo Kijak <gk46 at duke.edu> wrote:
>> Dear Mark,
>> 
>> I’m new to microarray data analysis but have a strong background in Biology.
>> 
>> I inherited a gene expression log2-transformed dataset produced in Illumina
>> (FinalReport_AVGSignal) and I was able to import it and quantile- normalize
>> it in Partek.
>> 
>> As I have relatively few samples, I think that I should do the analysis with
>> Limma rather than t-test and ANOVA implemented in Partek.
>> 
>> Is there a simple way for me to import the normalized
>> “FinalReport_AVGSignal” file into beadarray, so that I can run Limma in it?
>> Thanks,
>> 
>> Gustavo
>> 
>> Gustavo Kijak,
>> 
>> Duke University
>> 
>> 
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


______________________________________________________________________
The information in this email is confidential and intend...{{dropped:6}}