On Nov 30, 2011 5:22 PM, "Kripa R" <kripa777@hotmail.com> wrote:
>
>
> Hello forum,
> Outline of my analysis: lumi for pre-processing and filtering, then i
take a subset of the normalized group and run this through limma.
> I've noticed that if i select my subset differently, the topTable
generated after limma differs. ie rather than select=c(1,2,3,4,5,6) it is
changed to select=c(1,4,3,2,5,6)  the final topTable differ although the
samples input are actually identical
> Does this mean that the subset order must be identical to that in the
targets file? Or have I missed something in my current limma code (see
below)?
> I believe I'm currently lacking a line which would indicate which sample
fits in each spot of the model.matrix, if that makes sense?
>

Yes.  The targets and sample info need to be in the same order and you are
responsible for making sure that is the case.  While it is a bit more work,
I highly recommend constructing an ExpressionSet to avoid ordering errors
and to keep the sample info and data together.

Sean

> Any help would be greatly appreciated!!
>
>
> example of my code.
> subset <- subset(selDataMatrix, select=c(1,2,3,4,5,6));
>
> targets<-read.csv("targets.csv", skip=7);
> targets
> Sample_Name   Sample_Group   Pairs   Sentrix_ID   Sentrix_Position
> 1                       T                      1
> 2                       C                      2
> 3                       C                      1
> 4                       T                      2
> 5                       T                      3
> 6                       C                      3
>
>
> clinical <- factor(targets$Sample_Group);
> individual <- factor(targets$Pairs);
>
> design <- model.matrix(~1+clinical+individual)
> #design headers appear are as followe: (Intercept)    clinicalT
individual2   individual3
>
> fit <- lmFit(subset, design);
> ebayes <- eBayes(fit);
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>
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