Hello ! To get the intensities of R and G channel I use RG.MA() on normalized data set. I can calculate the standard deviation using simple function sd( ). But there the spot duplicates are not taken into account, only slide replicates. After running lmFit(), eBayes() and topTable() the duplicates are accounted. But how can I get from that results the standard deviation? Does it correspond to $stdev.unscaled from lmFit() output and can I use that for simple graphics (like R to G channel with sd-bars)? Thanks ! Sebastian Thieme

Is this what you want for R and G channel simple graphics? RGnorm <- RG.MA(MA) # on raw scale # log2 scale standard deviations for each row in R, G matrix logRsd <- apply(log2(RGnorm$R), 1, sd, na.rm=T) logGsd <- apply(log2(RGnorm$G), 1, sd, na.rm=T) The error components in lmFit, eBayes fit are for the MA$M fitted values, fit$coef. Marcus >>> Sebastian Thieme <tobar@gmx.de> 4/02/2005 12:21:04 PM >>> Hello ! To get the intensities of R and G channel I use RG.MA() on normalized data set. I can calculate the standard deviation using simple function sd( ). But there the spot duplicates are not taken into account, only slide replicates. After running lmFit(), eBayes() and topTable() the duplicates are accounted. But how can I get from that results the standard deviation? Does it correspond to $stdev.unscaled from lmFit() output and can I use that for simple graphics (like R to G channel with sd-bars)? Thanks ! Sebastian Thieme _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}

>Date: Fri, 04 Feb 2005 00:21:04 +0100 >From: Sebastian Thieme <tobar@gmx.de> >Subject: [BioC] LIMMA: How do I get the standard deviation? >To: bioconductor@stat.math.ethz.ch >Message-ID: <6.2.0.14.0.20050204000430.02c8eeb0@mail.gmx.net> >Content-Type: text/plain; charset="us-ascii"; format=flowed > >Hello ! > >To get the intensities of R and G channel I use RG.MA() on normalized data >set. >I can calculate the standard deviation using simple function sd( ). But >there the spot duplicates are not taken into account, only slide replicates. >After running lmFit(), eBayes() and topTable() the duplicates are accounted. >But how can I get from that results the standard deviation? Standard deviation of what? >Does it correspond to $stdev.unscaled from lmFit() output and can I use >that for simple graphics (like R to G channel with sd-bars)? sd-bars of what? Gordon >Thanks ! > >Sebastian Thieme