Hi Mick,
If the replicate spots are printed in a systematic way (eg
side-by-side), then lmFit() can be used to do the averaging.
For example
MA <- new("MAList", list(M=matrix(rnorm(60), 10, 6),
A=matrix(rnorm(60,
8, 2), 10, 6)))
is a random MAList object of 6 arrays with 10 genes on each. Assuming
the duplicate spots are printed side by side in the rows of a print-
tip
group ,
aveMdups <- lmFit(MA, design=diag(1, dim(MA)[2]), ndups=2, spacing=1)
will average over the duplicate spots, with the values stored in
aveMdups$coef
You can change the 'spacing' argument if the duplicate spots are
printed
in another way. A similar approach can be used to average the A
values:
aveAdups <- lmFit(MA$A, design=diag(1, dim(MA)[2]), ndups=2,
spacing=1)
Best wishes,
Matt
michael watson (IAH-C) wrote:
>Hi
>
>The title says it all really - how do I average over replicate spots
>from an MA object in limma?
>
>Thanks
>Mick
>
