Jim, Thank you very much for your reply. Page 50 of my copy of the document talks about the targetsA2C function, which we attempted to use. It appeared to properly convert the targets object, however when we called read.maimages with the new targets the result was data duplication of both red and green signal. This duplication is propagates to the MAList object after normalization. Possibly, this duplication gets resolved if we were to use the lmfit feature. Unfortunately we are using limma to do background correction and normalization only and we use other tools to analyze the resulting data matrix. Sincerely, Boris Umylny On Thursday 29 January 2009 11:03:45 pm James W. MacDonald wrote: > Hi Boris, > > Does the example of how to do this in the limma User's Guide (starting > on p. 50) not suffice? > > Best, > > Jim > > Boris Umylny wrote: > > Thank you in advance for your help. > > > > We are trying to use limma package to extract and normalize Agilent > > 2-channel data. Our objective is to use a single 2-channel chip as 2 > > 1-channel chips. > > > > We attempted the following: > >> library(limma) > >> targets <- readTargets("targets_file", row.names = "Name") > >> RG <- read.maimages(...) > >> RG.c <- backgroundCorrect(...) > > > > At this point we have an RG and RG.c objects that contains information > > for both channels. > > > >> MA <- normalizeWithinArrays(...) > > > > At this point, the two channel data has been replaced by a single value. > > > > We tried to use targetsA2C to convert to 1-channel design: > >> targets.1 <- targetsA2C(targets) > >> RG <- read.maimages(targets.1 ...) > > > > However, that simply duplicated Red and Green values. For 3 chips we had a set of 3 red and 3 green duplicates. So, once we get to: > >> MA <- normalizeWithinArrays(...) > > > > We have 6 values, but these 6 values are 3 sets of duplicates. > > > > How would we go about getting a set of normalized values from each > > channel of a 2-channel chip using limma? > > > > > > Sincerely, > > > > > > Boris Umylny > > > > > > > > > > > > [[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

Dear Alex, Thank you very much for your kind reply. The RG.MA function is exactly what we were looking for. I am sorry to trouble you with such a trivial question. Thank you again. Sincerely, Boris Umylny On Thursday 29 January 2009 05:57:03 pm Axel.Klenk at actelion.com wrote: > Dear Boris, > > see ?RG.MA from limma or the RG.MA code for computing normalized RG from > MA, i.e. > > > RG.MA > > function (object) > { > object$R <- 2^(object$A + object$M/2) > object$G <- 2^(object$A - object$M/2) > object$M <- NULL > object$A <- NULL > new("RGList", unclass(object)) > } > <environment: namespace:limma=""> > > Cheers, > > - axel > > > Axel Klenk > Research Informatician > Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / > Switzerland > phone +41 61 565 6367 / fax +41 61 565 6470 / axel.klenk at actelion.com / > www.actelion.com > > > > > Boris Umylny > <umylny at="" apbri.org=""> > > To > > Sent by: bioconductor at stat.math.ethz.ch > bioconductor-boun cc > ces at stat.math.eth > z.ch Subject > [BioC] Limma: Question about > extracting 2-channel data > 29.01.2009 09:33 > > > > > > > > > > Thank you in advance for your help. > > We are trying to use limma package to extract and normalize Agilent > 2-channel data. Our objective is to use a single 2-channel chip as 2 > 1-channel chips. > > We attempted the following: > > library(limma) > > targets <- readTargets("targets_file", row.names = "Name") > > RG <- read.maimages(...) > > RG.c <- backgroundCorrect(...) > > At this point we have an RG and RG.c objects that contains information for > both channels. > > > MA <- normalizeWithinArrays(...) > > At this point, the two channel data has been replaced by a single value. > > We tried to use targetsA2C to convert to 1-channel design: > > targets.1 <- targetsA2C(targets) > > RG <- read.maimages(targets.1 ...) > > However, that simply duplicated Red and Green values. For 3 chips we had a > > set of 3 red and 3 green duplicates. So, once we get to: > > MA <- normalizeWithinArrays(...) > > We have 6 values, but these 6 values are 3 sets of duplicates. > > How would we go about getting a set of normalized values from each channel > of a 2-channel chip using limma? > > > Sincerely, > > > Boris Umylny > > > > > > [[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 > > > > > The information of this email and in any file transmitted with it is > strictly confidential and may be legally privileged. It is intended solely > for the addressee. If you are not the intended recipient, any copying, > distribution or any other use of this email is prohibited and may be > unlawful. In such case, you should please notify the sender immediately and > destroy this email. The content of this email is not legally binding unless > confirmed by letter. Any views expressed in this message are those of the > individual sender, except where the message states otherwise and the sender > is authorised to state them to be the views of the sender's company. For > further information about Actelion please see our website at > http://www.actelion.com