[BioC] marray and limma error with lmFit

[Gordon K Smyth]

Dear Birger,

Don't forget to state your limma version when you ask a question.  Almost certainly you have a
slightly out of data version.  Reinstall limma and the example should work again, although with
changed column names for topTable.

Best wishes
Gordon

> Date: Thu, 19 Apr 2007 15:11:39 +0200
> From: "Hauchecorne Birger" <Birger.Hauchecorne at student.ua.ac.be>
> Subject: [BioC]   marray and limma error with lmFit
> To: <bioconductor at stat.math.ethz.ch>
> Cc: birgerhauchecorne at hotmail.com
> Message-ID:
> 	<A4E682B8A936374A9190A3A0FEE412F22D18DB at xmail10.ad.ua.ac.be>
> Content-Type: text/plain
>
> 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 at 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