Hi, 
 
I've got a little problem with lmFit and I was hoping you could help me.
 
I'm following a book in order to analyse microarray data. The book I follow is "Bioinformatics and Computational Biology Solutions Using R and Bioconductor" by Gentleman et al.. More precise chapter 4 "Preprocessing Two-Color Spotted Arrays" by Yang and Paquet.
In order to get used to the protocol, I followed the example used in the book.
These are the procedures used:
>library(beta7)
>library(arrayQuality)
>Targetinfo<-read.marrayInfo("TargetBeta7.txt")
>mraw<-read.GenePix(targets=Targetinfo)
>normdata<-maNorm(mraw)
>library(convert)
>mdata<-as(normdata,"exprSet")
 
And then in the book, they used this:
>LMres<-lmFit(normdata,design=c(1,-1,-1,1,1,-1),weights=NULL)
Error in fit$Amean <- rowMeans(unwrapdups(object@maA, ndups = ndups, spacing = spacing),  : 
        object "fit" not found
 
giving me an error.
 
I searched for this in the net, and found a solution from you
>LMres<-lmFit(as(normdata,"MAList"),design=c(1,-1,-1,1,1,-1),weights=NULL)
 
So I could continue with
>LMres<-eBayes(LMres)
>restable<-topTable(LMres,number=10,resort.by="M")
Error in order(na.last, decreasing, ...) : 
        argument 1 is not a vector
 
giving me another error. I can't sort by M (a parameter I need)
By sorting on another parameter ("T" for example), I could generate a list nonetheless. In the book there was a solution for the analysis, so I checked it with the list I found. Oddly enough the values found for "M" in the book where equal to my "logFC" values, unfortunately I couldn't sort on "logFC".

Another odd thing that I found was the the resulting P.Value from the book (which was 1 for the significant cases), was different from my P.Values (although the genes are the same). Most of the time where it was supposed to be 1, I became 0. Unfortunately again, not all the time, so it was impossible to tell where it was correct.
 
I'm now thinking that the cause of this problem can be found in the solution you guys gave for the first problem (>LMres<-lmFit(as(normdata,"MAList"),design=c(1,-1,-1,1,1,-1),weights=NULL))
 
I was hoping you could help me with my problem why these P.values are different, and where is my "M" column?
 
 
I'm using R 2.4.1. on windows XP having installed bioconductor.
 
Kind regards and thanks in advance,
 
Birger Hauchecorne
Senior Student Bio-Engineering at University of Antwerp, Belgium
 
 

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