[BioC] Limma: Question about extracting 2-channel data

[Boris Umylny]

Jim,

Thank you very much for your reply.

Page 50 of my copy of the document talks about the targetsA2C function, which 
we attempted to use.  It appeared to properly convert the targets object, 
however when we called read.maimages with the new targets the result was data 
duplication of both red and green signal.  This duplication is propagates to 
the MAList object after normalization.

Possibly, this duplication gets resolved if we were to use the lmfit feature.  
Unfortunately we are using limma to do background correction and 
normalization only and we use other tools to analyze the resulting data 
matrix.

Sincerely,

Boris Umylny


On Thursday 29 January 2009 11:03:45 pm James W. MacDonald wrote:
> Hi Boris,
>
> Does the example of how to do this in the limma User's Guide (starting
> on p. 50) not suffice?
>
> Best,
>
> Jim
>
> Boris Umylny wrote:
> > Thank you in advance for your help.
> >
> > We are trying to use limma package to extract and normalize Agilent
> > 2-channel data.  Our objective is to use a single 2-channel chip as 2
> > 1-channel chips.
> >
> > We attempted the following:
> >> library(limma)
> >> targets <- readTargets("targets_file", row.names = "Name")
> >> RG <- read.maimages(...)
> >> RG.c <- backgroundCorrect(...)
> >
> > At this point we have an RG and RG.c objects that contains information
> > for both channels.
> >
> >> MA <- normalizeWithinArrays(...)
> >
> > At this point, the two channel data has been replaced by a single value.
> >
> > We tried to use targetsA2C to convert to 1-channel design:
> >> targets.1 <- targetsA2C(targets)
> >> RG <- read.maimages(targets.1 ...)
> >
> > However, that simply duplicated Red and Green values.  For 3 chips we had 
a set of 3 red and 3 green duplicates.  So, once we get to:
> >> MA <- normalizeWithinArrays(...)
> >
> > We have 6 values, but these 6 values are 3 sets of duplicates.
> >
> > How would we go about getting a set of normalized values from each
> > channel of a 2-channel chip using limma?
> >
> >
> > Sincerely,
> >
> >
> > Boris Umylny
> >
> >
> >
> >
> >
> > 	[[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor