Hi, Avinash. You might try the virtualArray package. I have never used it, but it aims to solve problems such as yours. Sean On Mon, Mar 11, 2013 at 1:08 AM, avinash sethi <avicct at="" gmail.com=""> wrote: > One dataset is from ATH1-affymatrix genechip and another from cDNA- array. > Each dataset has 4 biological replicates at each time point (0hpi,24hpi). In > total, there are 8 and 4 assays from above two platform respectively. > In cDNA-array, common reference was labeled with Cy3 and Cy5 was used to > label 0hpi or 24 hpi. > I want to integrate these two datasets at raw intensity level and then do > downstream analysis (normalization, batch effect removal, differential > expression). > -array > > > On Mon, Mar 11, 2013 at 2:02 AM, Sean Davis <seandavi at="" gmail.com=""> wrote: >> >> What is the experimental design on the two platforms? What comparisons do >> you want to make? >> >> On Mar 10, 2013 1:57 PM, "Avinash [guest]" <guest at="" bioconductor.org=""> wrote: >>> >>> >>> Hi, >>> I am trying to intermingle two timeseries expression data from two >>> different platform (affymatrix and cDNA array).To follow a common index >>> system, I mapped the probesets and cDNA clones (from above given platforms, >>> respectively) to unique entrez Ids. Only common Ids are retained (~7500). >>> How can I integrate or compare these two datasets together at intensity >>> level? >>> >>> >>> -- output of sessionInfo(): >>> >>> >>> R version 2.15.2 (2012-10-26) >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_IN >>> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_IN >>> LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C >>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> _______________________________________________ >>> 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 > >