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

[Mark Dunning]

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
>
>