why not?
 
... the usual and then
con.matrix<- matrix( -1/69, 70, 70)
for (i in 1:70){ cm[i,i]<-1}
 
colnames (con.matrix)<- levels (myClasses)
 
fit2<- contrasts.fit (fit1, con.matrix)
fit2<-eBayes(fit2)
 
topTable (fit2, coef=65, genelist=whatever)
 
 

________________________________

From: bioconductor-bounces@stat.math.ethz.ch on behalf of Lana Schaffer
Sent: Tue 11/09/2007 22:46
To: Naomi Altman; bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] analysis of 70 groups for differential expression



Naomi,
Yes, you are correct.
Lana

-----Original Message-----
From: Naomi Altman [mailto:naomi@stat.psu.edu]
Sent: Tuesday, September 11, 2007 2:19 PM
To: Lana Schaffer; bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] analysis of 70 groups for differential expression

If I understand you correctly, this is one-way ANOVA with 69 contrasts,
not 69 separate ANOVAs (or t-tests).  I.e. 1 run of limma with a huge
contrast matrix.

--Naomi

At 12:14 PM 9/11/2007, Lana Schaffer wrote:

>Hi,
>We have a situation were there are 70 groups and we want to know if
>there is differential expression in a group.  I think of the problem as

>contrasting the expression of 1 group and the rest of the groups.
>In this case, limma would need to done 70 times for each group contrast

>versis the rest of the groups.
>But this would result in an uneven comparison between one group and 70
>other groups.  Can someone suggest a way to approach this problem?
>
>Lana Schaffer
>Biostatistics/Informatics
>The Scripps Research Institute
>DNA Array Core Facility
>La Jolla, CA 92037
>(858) 784-2263
>(858) 784-2994
>schaffer@scripps.edu
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor@stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>Search the archives:
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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