[BioC] mergeScans function in limma - minFactor error

[Agnieszka Żmieńko]

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