On Wed, Dec 3, 2008 at 3:17 AM, santana sarma <aimanusarma at="" gmail.com=""> wrote: > Thanks ! > > Well, it is the simplest type of microarray experiment, with replicate > two-color arrays of the same two RNA sources. It has its dyes swapped for > one of the arrays: > > ------------------------------------------------------------- > > File cy3 cy5 > > ------------------------------------------------------------- > > a wt mu > > b wt mu > > c_DyeSwap mu wt > > > > Wonder how to go for the annotated output for my gene list (before > downstream statistical analysis). User guides of LIMMA and others mainly > focus on how to obtain statistics with regards to differential expression et > al. The annotation is in RG$genes. You can make a data.frame that includes the gene annotation and your values using cbind(). Then, you can use write.csv on that data.frame to make a text file. Sean > On Wed, Dec 3, 2008 at 3:42 AM, Naomi Altman <naomi at="" stat.psu.edu=""> wrote: > >> Dear Santana >> >> This does not really help much, because the "normalized expression" depends >> on the treatment. Do both channels have the same treatment? Is this a >> reference design? >> >> Anyways, to do what you want, what I generally do is use cbind to merge the >> expression values with the annotation information and write.csv to write a >> comma separated table which can be read into a spreadsheet such as Excel. I >> do not expect to be able to do all my processing in R. However, some of the >> R gurus on the list can probably do everything in R. I meant >> to cc the list when I first wrote, and I am returning this to you. >> >> Best of luck, >> Naomi >> >> >> At 04:31 AM 12/2/2008, you wrote: >> >> Hi Naomi, >> >> Thanks for your prompt reply ! >> >> Well, I wanted to experiment something, and accordingly thought that I >> would examine the individual raw data. But I believe, I should follow the >> conventional way, atleast for the time-being. >> >> Anyways, even then I have a bit of problem. >> >> I am uncertain as to how I can have each gene's normalised expression along >> with its annotation in one file. I am able to do it for Affymetrix data >> which is not very complicated, but I'm having problems in trying to do it >> with cDNA microarrays (for 3-biological replicates where one of them is a >> dye-swap). >> >> Let's say, in a nutshell, I have already done with the following : >> >> library(arrayQuality); library(graphics); library(RColorBrewer) >> >> targets <- readTargets("target77.txt") >> >> files <- c("a.gpr", "b.gpr", "c_DyeSwap.gpr") # Suppose >> these are my files >> >> RG <- read.maimages (files,source="genepix") >> >> RG$printer <- getLayout(RG$genes) # to set print >> layout >> >> RG.b <- backgroundCorrect(RG) >> >> MA.RG <- normalizeWithinArrays (RG.b) >> >> MA.BT <http: ma.bt=""/> <- normalizeBetweenArrays (MA.RG) >> >> design <- c(1,1,-1) >> >> # from here, I don't know how to move ahead that would give me a file >> (.HTML/.csv) that would contain each gene's normalised expression with its >> annotation. >> >> I would highly appreciate your suggestion(s). >> >> Thanks !! >> >> Kind regards, >> >> Santana >> = = = = = = = = = >> >> On Tue, Dec 2, 2008 at 5:43 PM, Naomi Altman <naomi at="" stat.psu.edu=""> wrote: >> Are you sure you want the RAW intensities. That would mean unaltered >> data. I think you want a normalized >> mean intensity. You could do that in limma using the single channel >> analysis. Limma can produce means - not just differences. >> >> Naomi Altman >> >> >> At 11:23 PM 12/1/2008, you wrote: >> Hi All, >> >> I am in need of some basic 2-color (cDNA) microarray help. >> >> With 3-biological replicates (one of them is a dye-swap), I wish to merge >> ONLY the raw intensities of the 3 cDNA files. This merging should take into >> account of the dye-swap file too. Finally, it should produce an HTML (or, >> CSV) file that contains ONE raw expression against each available gene with >> the relevant annotation. >> >> I am not confident as to how I should script it. I did go through some >> packages like LIMMA, but couldn't really extract what I wanted, as they >> focus mainly on statistics for differential expression. >> >> Thank you ! >> >> Cheers, >> Santana >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> Naomi S. Altman 814-865-3791 (voice) >> Associate Professor >> Dept. of Statistics 814-863-7114 (fax) >> Penn State University 814-865-1348 (Statistics) >> University Park, PA 16802-2111 >> >> Naomi S. Altman 814-865-3791 (voice) >> Associate Professor >> Dept. of Statistics 814-863-7114 (fax) >> Penn State University 814-865-1348 (Statistics) >> University Park, PA 16802-2111 >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >