[BioC] Error with ImaGene out put file in limma

[Gordon K Smyth]

> 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))

You have 3 arrays but you've given 4 numbers. You need just
design=c(-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.

You only have one comparison to make: BCYE vs XDM, so there is only
coefficient, regardless of number of arrays.

Gordon

>
> 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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>
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