[BioC] mergeScans functions in limma - minFactor error

[Gordon K Smyth]

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

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