[BioC] LIMMA : design (1, 2, 3, 3 ) , I got EXCITING results, what could be the logic, since i have 2 replicates for 3rd group only ?

[Saurin Jani]

Hi Adai,

Yes, you are right. I have 4 samples : 

Group1 = Growth Effect for Day 1 : 1 Affy GeneChip.
Group2 = Growth Effect for Day 2 : 1 Affy GeneChip.
Group3 = Growth Effect for Day 3 : 2 Affy GeneChips.

so, my design matrix is: 
design <- model.matrix(~ -1+factor(c(1,2,3,3)));

LIMMA did not give any error or waring even it has 1
sample per group...! ( I thought similar thing,  since
it needs technical replicates per group to make a
decision). The results are very interesting. I have
many genes for 0.01 FDR, which is very good.  

Somehow,I don't understand the logic. Do you think is
this a valid design? Or You think I should go by Fold
Change Logic. Please, let me know. 

Thank you very much,
Saurin





--- Adaikalavan Ramasamy <ramasamy at cancer.org.uk>
wrote:
> PLEASE correct me if I am wrong. 
> 
> You have a total of 4 samples that could be
> classified into one of 3
> groups ? How do you plan on distinguishing
> biological from technical
> variation ? Shouldn't limma come with some sort of
> warning or error if
> there are only one sample per group ?
> 
> Regards, Adai
> 
> 
> 
> On Tue, 2005-04-26 at 10:01 -0700, Saurin Jani
> wrote:
> > Hi BioC,
> > 
> > I have 3 groups but I have only 2 replicates for
> last
> > group. so, group 1 and 2 has only one Affy CEL
> file. I
> > Did..LIMMA as below and I got some Exciting
> results:
> > 
> > #----------------------------------
> > design <- model.matrix(~ -1+factor(c(1,2,3,3)));
> > colnames(design) <-  c("g1","g2","g3");
> > fit <- lmFit(myRMA,design);
> > 
> > contrast.matrix <-
> > makeContrasts(g1-g2,g1-g3,g2-g3,levels = design);
> > 
> > fit2 <- contrasts.fit(fit,contrast.matrix);
> > fit2 <- eBayes(fit2);
> > 
> > results <-
> > decideTests(fit2,adjust="fdr",p.value=0.01);
> > 
> > myGenes <- geneNames(myRMA);
> > i <- apply(results,c(1,2),all);
> > 
> > a <- i[,1];
> > b <- i[,2];
> > c <- i[,3];
> > tempgenes1 <- myGenes[a];
> > tempgenes2 <- myGenes[b];
> > tempgenes3 <- myGenes[c];
> > 
> > tempall <- c(tempgenes1,tempgenes2,tempgenes3);
> > myDEGenes <- tempall;
> > 
> > esetSub2X <- MatrixRMA[myDEGenes,];
> > esetSub2 <- new("exprSet",exprs = esetSub2X);
> > pData(esetSub2) <- pData(myRMA);
> > heatmap(esetSub2X); 
> > #----------------------------------
> > 
> > I got EXCITING results, what could be the
> logic,since
> > i have 2 replicates for 3rd group only ?
> > 
> > Could anyone point me out ? 
> > 
> > I highly appreciate your help , Thank you in
> advance. 
> > 
> > Thank you,
> > Saurin
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > 
> 
>