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 > >

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}}