[BioC] swaping values in a RGList object...

[Marcus Davy]

Another way would be to modify/correct the "targets" descriptor information which relates the treatments to the Cy3 and Cy5 channels for each slide without having to reorder intensity information within the GRList at all.

Targets information is in section 5.2 of the limma users guide, limmaUsersGuide().

Marcus

>>> Richard Pearson <Richard.Pearson at postgrad.manchester.ac.uk> 1/07/2005 1:19:26 p.m. >>>
Lourdes,

Try the following:

R1 <- RG$R[,1]
R2 <- RG$R[,2]
RG$R[,1] <-R2
RG$R[,2] <-R1

Regards

Richard


Quoting Lourdes Peña Castillo <lourdes.pena at gmail.com>:

> Hello Everyone,
>
> I am analyzing micro-array data using limma, and I need to swap
> intensity data between arrays  (because the samples were mislabeled) .
> Something like:
>
> R1 <- RG[,1]$R
> R2 <- RG[,2]$R
> RG[,1]$R <-R2
> RG[,2]$R <-R1
>
> But I get the message:
>
>  Error: incorrect number of subscripts on matrix
>
> I have also tried replacing the values using  a for-loop but got the
> same error.
>
> for (i in 1:length(RG[,1]$R)) {
>  RG[,1]$R[i] <- R2[i]
> }
>
> Do you know how I can swap the values?
>
> Thanks!
>
> Lourdes
>
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