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

[Sean Davis]

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
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>