[BioC] mergeScans function in limma - minFactor error

[Henrik Bengtsson]

Not answering your specific questions, but an alternative is to use:

library("aroma.light");
r <- calibrateMultiscan(R);
g <- calibrateMultiscan(G);

where R is an JxK matrix holding the K scans of the J (foreground)
signals in the red channel.  The calibrated/merged output is a Jx1
matrix.  Likewise, G is a JxK matrix for the green channel with the
merged signals in 'g' (a Jx1 matrix).  Use foreground signals only -
do not use background corrected signals.

There is no need for tuning parameters.  It works out of the box
(unless "funny" things were done during scanning).  See
help("calibrateMultiscan.matrix", package="aroma.light") for further
help and explanation.  Further details, figures and results can be
found in:

H. Bengtsson, J. Vallon-Christersson and G. Jönsson, Calibration and
assessment of channel-specific biases in microarray data with extended
dynamical range, BMC Bioinformatics, 5:177, 2004.
http://www.biomedcentral.com/1471-2105/5/177/

/Henrik

2012/1/26 Agnieszka Żmieńko <akisiel at ibch.poznan.pl>:
> 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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