[BioC] Limma:Single Channel Normalization for two color Arrays

[Ranga Chari]

Hi, 
 I shmelessly accept that I might be stupid by asking
a simple question ( I am new to microarray data
analysis) 
 When you have done your experiment using Cy5 and Cy3
dyes then you might have used either cDNA or a long
oligo chip.  That means this is a two channel array. 
Then why do you want to normalize single channel.

Is this a process of within array normalization or
some  bypass methods to avoid complexities. 
can you please let me know. 

Thank you.

Ranga


--- Sean Davis <sdavis2 at mail.nih.gov> wrote:
> Binita,
> 
> I hope Gordon Smyth doesn't mind my quoting him
> (from a previous response to
> the same question):
> 
> "...On reading your question again, I'm guessing
> that you're wanting the
> normalized single-channel red and green intensities.
> Is this right? If so,
> you can get them from
> 
> RG <- RG.MA(MA)
> 
> (see the last section of the Limma User's Guide)
> where MA is the normalized
> MAList object, then write RG$R and RG$G to file. Or
> possibly form
> cbind(RG$G,RG$R) and write that to one file...."
> 
> There are multiple other responses to the list in
> the past regarding
> transforming MA back to RG.
> 
> Hope this helps.
> 
> Sean
> 
> On 6/30/04 4:56 AM, "Binita Dutta"
> <binita.dutta at vib.be> wrote:
> 
> > Dear All,
> > 
> > I have done single channel normalization for 8
> arrays.
> > 
> >  Sl.No. Slide.Name        Cy5        Cy3
> > 1      1 2003110429  J  2 0min      J2 30min
> > 2      2 2003110430  J2 0min        J3 0min
> > 3      3 2003110431  J2 30min      J3 30min
> > 4      4 2003110432  J3 0min        J3 30min
> > 5      5 2003110433  J2 30min      J2 0min
> > 6      6 2003110434  J3 0min        J2 0min
> > 7      7 2003110435  J3 30min      J2 30min
> > 8      8 2003110436  J3 30min      J3 0min
> > 
> > Can we used the normalized intensities (red and
> green channel) instead of
> > normalized MA, to determine differentially
> expressed genes with design
> > matrix  similar to what we use for analysis for
> Affymetrix data.
> > 
> > I have been unable to export normalized Green and
> Red channel intensities.
> > 
> > However, when i use following commands, I get M
> and A values.
> > 
> > 
> > write.table(MA.p$A,file="h:\\r\\Exp200\\single
> channel nor A.txt", append
> > = FALSE, sep = "\t", eol="\n", na="NA", dec="")
> > write.table(MA.p$M,file="h:\\r\\Exp200\\single
> channel nor M.txt", append
> > = FALSE, sep = "\t", eol="\n", na="NA", dec="").
> > 
> > Please suggest me how can i export normalized red
> and green channel
> > intesities.
> > 
> > 
> > I have other experiments to analyse and would like
> to use single channel
> > normalization.
> > 
> > Thanks in advance
> > 
> > Binita
> > 
> > 
> > 
> > ==============================
> > 
> > Binita Dutta, PhD
> > MicroArray Facility(MAF)
> > UZ Gasthuisberg
> > Onderwijs en Navorsing
> > Herestraat 49
> > 3000 Leuven
> > Belgium
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> >
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https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
> 
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