Hi, I was hoping that someone might be able to help me. I have inherited data from 4 Agilent arrays. I would like to recover and output to file the normalised signal intensity of the Cy3 and Cy5 data if possible, rather than the log ratio of each. If anyone can suggest a way to do this I would be most grateful. As the MA can be use by plotDensities() to show the effect of normalisation upon signal intensities, I'm hoping that this will be possible. Hope you can help. Best wishes, Bryony [[alternative HTML version deleted]]

On Fri, May 7, 2010 at 12:04 PM, Lloyd, Bryony <bryony.lloyd at="" liverpool.ac.uk=""> wrote: > Hi, > > I was hoping that someone might be able to help me. I have inherited data from 4 Agilent arrays. I would like to recover and output to file the normalised signal intensity of the Cy3 and Cy5 data if possible, rather than ?the log ratio of each. If anyone can suggest a way to do this I would be most grateful. > As the MA can be use by plotDensities() to show the effect of normalisation upon signal intensities, I'm hoping that this will be possible. > Hope you can help. See the RG.MA in limma, assuming that you have an MAList. If not, you'll need to be more specific about what you have. Sean

On Sat, May 8, 2010 at 6:22 AM, Lloyd, Bryony <bryony.lloyd@liverpool.ac.uk>wrote: > > Hi, > > Many thanks for your kind help. My first day with Bioconductor has been > interesting to say the least. I have created my RGList from my normalised > MAList, and have managed to write the $R and $G data to file by creating > sublists, representing the data as a matrix (as.matix) and writing this to > file. As this does not work with text I need to get hold of the $genes data > somehow I would be delighted if someone could help. > > If your RGlist is called RG: write.table(RG$genes,"genes.txt",sep="\t",col.names=TRUE,row.names=FAL SE) Sean > ________________________________________ > From: Sean Davis [seandavi@gmail.com] > Sent: 07 May 2010 17:44 > To: Lloyd, Bryony > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] Obtaining Normalised Signal intensities > > On Fri, May 7, 2010 at 12:04 PM, Lloyd, Bryony > <bryony.lloyd@liverpool.ac.uk> wrote: > > Hi, > > > > I was hoping that someone might be able to help me. I have inherited data > from 4 Agilent arrays. I would like to recover and output to file the > normalised signal intensity of the Cy3 and Cy5 data if possible, rather than > the log ratio of each. If anyone can suggest a way to do this I would be > most grateful. > > As the MA can be use by plotDensities() to show the effect of > normalisation upon signal intensities, I'm hoping that this will be > possible. > > Hope you can help. > > See the RG.MA in limma, assuming that you have an MAList. If not, > you'll need to be more specific about what you have. > > Sean > [[alternative HTML version deleted]]