[BioC] Error with ImaGene out put file in limma

[Marcelo Luiz de Laia]

Hi Pete,

Thanks very much!!! Your helps was very good!

Now, I have another problem.

I execute the commands above and have this result:

>
RegianeSample<-read.table("regianeRicoPobre.txt",header=TRUE,sep="\t",as.is=
TRUE)
> RegianeSample
  SlideNamber            FileNameCy3            FileNameCy5  Cy3  Cy5
1           1 lamina1_0_selected.txt lamina1_1_selected.txt  XDM BCYE
2           2 lamina2_0_selected.txt lamina2_1_selected.txt BCYE  XDM
3           3 lamina3_0_selected.txt lamina3_1_selected.txt BCYE  XDM
> slides<-cbind(RegianeSample$FileNameCy3, RegianeSample$FileNameCy5)
> RG <- read.maimages(slides, source="imagene")
Read header information
Read lamina1_0_selected.txt
Read lamina1_1_selected.txt
Read lamina2_0_selected.txt
Read lamina2_1_selected.txt
Read lamina3_0_selected.txt
Read lamina3_1_selected.txt
> show(RG)
All is correct !!
$printer
$ngrid.r
[1] 4
$ngrid.c
[1] 2
$nspot.r
[1] 32
$nspot.c
[1] 24
$genes
Is OK, too
> MA <- normalizeWithinArrays(RG)
> MA <- normalizeBetweenArrays(MA)
> ?lmFit
> fit <- lmFit(MA, design=c(-1,1,-1,1))
Error in lm.fit(X, y) : incompatible dimensions
> fit <- lmFit(MA, design=c(3,3,3,3))
Error in lm.fit(X, y) : incompatible dimensions
>

Here I have a problem?

I have 3 replicates (3 treated and 3 untread), that correspond to 3 arrays
(slides)!?. But I dont know how much coeficients I will be estimated.

Thanks

Marcelo
-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Pete
Sent: quarta-feira, 22 de outubro de 2003 13:44
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Error with ImaGene out put file in limma


Hi Marcelo
Having briefly looked through your script below i think what you need to do
is change


>slides <- RegianeSample$FileName

to something like

>slides<-cbind(RegianeSample$FileNameCy3, RegianeSample$FileNameCy5)

this should give you a list of the filenames of both the cy3 and cy5
samples. I hope this helps


Pete Underhill

Microarray Facility
MRC Harwell
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