Hi all!!

I am making a differential expression analysis of microarray data with two contrasts. My design matrix is like this

A_1 A_2 B

1 0 0

1 0 0

1 0 0

0 1 0

0 1 0

0 1 0

0 1 0

0 0 1

0 0 1

0 0 1

0 0 1

0 0 1

0 0 1

0 0 1

And my contrast matrix, made with the makeContrast function is this

Contrasts Levels A_1-B A_2 - B A_1 1 0 A_2 0 1 B -1 -1

I want to find the GO_terms associated to both contrasts, for that I am using the camera function like this

camera(Exprs, Index, design, contrast = contMatrix)

Where:

Exprs is my matrix of log-expression values

Index is the list of GO terms associated to the genes in the Exprs matrix

design is the design matrix I showed you before

and as contrast I input my contMatrix object i showed you before.

My doubt is if camera output is actually the GO_terms taking account the TWO contrasts defined.

If not, how can I get that result.

Thanks!!

Thank you Gordon,

Yes I got confused with the documentation...

What I want is the GO terms of both contrast, I think yes like a F-statistic. Do you know any library or function for that?

Thanks before hand,

Gaby

You could do an F-statistic topTable in limma, then pass the DE results to any gene ontology analysis package, such as gostats or goseq.

Alternatively, sticking to the limma package, you could run geneSetTest with the F-statistics for each GO set separately.

I haven't provided this functionality in camera() because camera() is designed to work with directional pathways and F-statistics are not directional. camera() is not designed to work with GO either, because of its redundancy and lack of directionality.