Using GOseq on Cuffdiff output

[sindrle]

Hi!
I have data from Cuffdiff, but do not understand how to do the following (from GOseq manual):

2 Reading data
We assume that the user can use appropriate in-built R functions (such as read.table or scan) to obtain two vectors, one containing all genes assayed in the RNA-seq experiment, the other containing all genes which are DE. If we assume that the vector of genes being assayed is named assayed.genes and the vector of DE genes is named de.genes we can construct a named vector suitable for use with goseq using the following:
> gene.vector=as.integer(assayed.genes%in%de.genes)
> names(gene.vector)=assayed.genes
> head(gene.vector)
It may be that the user can already read in a vector in this format, in which case it can then be immediately used by goseq.

Can anyone pls help? Thanks alot!!!

[nsl]

Hi sindrle,

Did you figure out how to input cuffdiff results into goseq?

Thanks
nsl

[sindrle]

The first steps I made an input looking like "genes" (see the manual), basically two columns, one with gene names and one with either 1 or 0 meaning DE or non-DE.

library(edgeR)
library(org.Bt.eg.db)
library(goseq)
library(GO.db)
library(annotate)

# 6.5 GO analysis
# 6.5.1 Fitting the Probability Weighting Function (PWF)
# #Getting gene length
pwf=nullp(MyoGenesGOseq,"hg19","geneSymbol")
pwfAdi=nullp(AdiGenesGOseq,"hg19","geneSymbol")

##6.5.2 Using the Wallenius approximation
GO.wall=goseq(pwf,"hg19","geneSymbol")
head(GO.wall)
GO.wallAdi=goseq(pwfAdi,"hg19","geneSymbol")
head(GO.wallAdi)

##6.5.6 Making sense of the results
enriched.GO=GO.wall$category[p.adjust(GO.wall$over_represented_pvalue, method="BH") < 0.1]

enriched.GOAdi=GO.wallAdi$category[p.adjust(GO.wallAdi$over_represented_pvalue, method="BH") < 0.13]

library(GO.db)

for(go in enriched.GO[1:5]){
print(GOTERM[[go]])
cat("--------------------------------------\n")
}

for(go in enriched.GOAdi[1:1]){
print(GOTERM[[go]])
cat("--------------------------------------\n")
}

[nsl]

Thank you for the quick reply Sindrle. I am new to this, may I bother you with a few more questions in the future if I get stuck?

sincerely,

nsl

[sindrle]

Well, I have just taken a quick look myself, but you can try!

[nsl]

Phew!

Sindrle, I thought i had my work cut out. I couldn't make head or tail of things at first. Very kind of you. I am going through the manual and shall incorporate your advice in the process. Thank you. It must be late in Norway!

[sindrle]

Good luck, keep us informed!!