Hi, I shmelessly accept that I might be stupid by asking a simple question ( I am new to microarray data analysis) When you have done your experiment using Cy5 and Cy3 dyes then you might have used either cDNA or a long oligo chip. That means this is a two channel array. Then why do you want to normalize single channel. Is this a process of within array normalization or some bypass methods to avoid complexities. can you please let me know. Thank you. Ranga --- Sean Davis <sdavis2@mail.nih.gov> wrote: > Binita, > > I hope Gordon Smyth doesn't mind my quoting him > (from a previous response to > the same question): > > "...On reading your question again, I'm guessing > that you're wanting the > normalized single-channel red and green intensities. > Is this right? If so, > you can get them from > > RG <- RG.MA(MA) > > (see the last section of the Limma User's Guide) > where MA is the normalized > MAList object, then write RG$R and RG$G to file. Or > possibly form > cbind(RG$G,RG$R) and write that to one file...." > > There are multiple other responses to the list in > the past regarding > transforming MA back to RG. > > Hope this helps. > > Sean > > On 6/30/04 4:56 AM, "Binita Dutta" > <binita.dutta@vib.be> wrote: > > > Dear All, > > > > I have done single channel normalization for 8 > arrays. > > > > Sl.No. Slide.Name Cy5 Cy3 > > 1 1 2003110429 J 2 0min J2 30min > > 2 2 2003110430 J2 0min J3 0min > > 3 3 2003110431 J2 30min J3 30min > > 4 4 2003110432 J3 0min J3 30min > > 5 5 2003110433 J2 30min J2 0min > > 6 6 2003110434 J3 0min J2 0min > > 7 7 2003110435 J3 30min J2 30min > > 8 8 2003110436 J3 30min J3 0min > > > > Can we used the normalized intensities (red and > green channel) instead of > > normalized MA, to determine differentially > expressed genes with design > > matrix similar to what we use for analysis for > Affymetrix data. > > > > I have been unable to export normalized Green and > Red channel intensities. > > > > However, when i use following commands, I get M > and A values. > > > > > > write.table(MA.p$A,file="h:\\r\\Exp200\\single > channel nor A.txt", append > > = FALSE, sep = "\t", eol="\n", na="NA", dec="") > > write.table(MA.p$M,file="h:\\r\\Exp200\\single > channel nor M.txt", append > > = FALSE, sep = "\t", eol="\n", na="NA", dec=""). > > > > Please suggest me how can i export normalized red > and green channel > > intesities. > > > > > > I have other experiments to analyse and would like > to use single channel > > normalization. > > > > Thanks in advance > > > > Binita > > > > > > > > ============================== > > > > Binita Dutta, PhD > > MicroArray Facility(MAF) > > UZ Gasthuisberg > > Onderwijs en Navorsing > > Herestraat 49 > > 3000 Leuven > > Belgium > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >