[BioC] Limma question: positive M values means upregulated in 'Treated' in this case?

[Jenny Drnevich]

Hi Wonjong,


>I think positive M values means upregulated in 'Treated' (group1), since
>I did group1 - group2 'Treated' - 'non-treated'. Is it correct?

Yes. If M is positive, that means group1 > group2, and if M is negative, 
group1 < group2

Cheers,
Jenny





>Or
>negative M value means upregulated in 'Treated'?
>
>library(limma)
>library(affy)
>data <- ReadAffy()
>eset <- rma(data)
>design <- model.matrix(~ -1+factor(c(1,1,1,1,2,2,2,2)))
>colnames(design) <- c("group1", "group2")
>fit <- lmFit(eset, design)
>contrast.matrix <- makeContrasts(group1-group2, levels=design)
>fit2 <- contrasts.fit(fit, contrast.matrix)
>fit2 <- eBayes(fit2)
>topTable(fit2, coef=1, adjust="fdr", sort.by="M", number=10)
>
>
>
>
>Thank you.
>
>Wonjong
>
> > design
>   group1 group2
>1      1      0
>2      1      0
>3      1      0
>4      1      0
>5      0      1
>6      0      1
>7      0      1
>8      0      1
>attr(,"assign")
>[1] 1 1
>attr(,"contrasts")
>attr(,"contrasts")$`factor(c(1, 1, 1, 1, 2, 2, 2, 2))`
>[1] "contr.treatment"
>
> >
>
>
>         [[alternative HTML version deleted]]
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>Search the archives: 
>http://news.gmane.org/gmane.science.biology.informatics.conductor

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu