Dear Agnieszka, My guess is that you need to background correct using backgroundCorrect() before using mergeScansRG(). If problems persist, I suggest you write directly to the function author. See help("mergeScansRG") for that info. Best wishes Gordon > Date: Thu, 26 Jan 2012 10:34:33 +0100 > From: Agnieszka ?mie?ko <akisiel at="" ibch.poznan.pl=""> > To: bioconductor at r-project.org > Subject: [BioC] mergeScans function in limma - minFactor error > Message-ID: <4F211E29.2000407 at ibch.poznan.pl> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Hello everyone. > > I am using limma for microarray analysis for some time. Now I am trying > to use mergeScans function to merge scans made with different laser > intensities. Each time I get the same error. I have tried to google- out > the solution but I do not much understand the discussions I've found. As > I am just a biologist and my R activity is mostly modifying commands > that I have found in the manuals or web., my question is - is there any > simple way to deal with it, without large programming skills and > knowledge (plese explain what kind of error is that, is it something > wrong with my data, what can I do) or do I need to find someone who > knows R better than me to help me overcome it? > > Thank you > > Agnieszka > > This is one of my trials - Agilent two-color arrays, scanned and > analyzed in GenePix: > > > RG1=read.maimages(targets1, source="genepix.custom", > other.columns=c("ControlType"), wt.fun = wtflags(weight=0, cutoff=-50)) > Custom background: MorphologicalOpening > Read 252162310143_1_of_0004_sat1_0635.gpr > > RG2=read.maimages(targets2, source="genepix.custom", > other.columns=c("ControlType"), wt.fun = wtflags(weight=0, cutoff=-50)) > Custom background: MorphologicalOpening > Read 252162310143_1_of_0004_0635.gpr > > > > RG1 <- mergeScansRG(RG2,RG1) > Error in nls(y ~ .hockey(x = x, alpha1, beta1, beta2, brk), start = > list(alpha1 = alpha1, : > step factor 0.000488281 reduced below 'minFactor' of 0.000976563 > > .pl ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}