[BioC] Re: Unequally spaced replicates in limma - "sort your MA object by gene ID "

[Saroj Mohapatra]

I know it is a basic R procedure - but what command would sort the
MAlist by gene ID?

> sort(MAlist, .....)?
Jakob

------------------------------------------------------
I tried this (for Imagene-output data). Is this correct?



o<-order(MA$genes$"Gene ID")
MA1<-list(R=MA$R[o], G=$MA$G[o], Rb=MA$Rb[o], Gb=$MA$Gb[o],
printer=MA$printer, weights=MA$weights[o], genes=MA$genes[o,]). 

I guess, we have to check the MAList, find the elements that are linked
to GeneID (in my case, R, Rb, G, Gb, weights, and genes) and copy them
in the sorted order. Others, such as, printer(layout), can be copied as
such.


I also have a related question. After sorting the MAList thus, is it
possible or even advisable to use the function duplicateCorrelation on
the sorted data?

Saroj 

Saroj Mohapatra
Wayne State University
Detroit USA