Using the edgeR manual, I'm trying to follow the examples to run the goana function. I run the glmQLFTest (without any issues) and then use its output "qlf" as the input for goana or the topTags(qlf). I get the following errors.
> qlf <- glmQLFTest(fit,coef=2) > go <- goana(qlf, species="Mm") Error in goana.default(de = DEGenes, universe = universe, ...) : No annotated genes found in universe > > toptags <- topTags(qlf, n=50) > go <- goana(toptags, species="Mm") Error in goana.default(toptags, species = "Mm") : components of de should be vectors > TT <- as.vector(toptags) > go <- goana(TT, species="Mm") Error in goana.default(TT, species = "Mm") : components of de should be vectors > toptags Coefficient: groups2 logFC logCPM F PValue FDR ENSMUSG00000028195 -3.3561168 7.661106 1076.90952 6.348826e-22 8.937877e-18 ENSMUSG00000006445 -1.7990272 7.681729 995.09376 1.651467e-21 1.162468e-17 ENSMUSG00000032531 -2.8981796 6.854250 878.57035 7.424919e-21 2.730134e-17 ENSMUSG00000022178 -1.6372362 6.168699 875.38451 7.757165e-21 2.730134e-17 ENSMUSG00000028967 -1.9122235 6.359604 842.42713 1.231471e-20 3.293641e-17 ENSMUSG00000028525 -2.1673682 5.400544 833.31214 1.403740e-20 3.293641e-17 ENSMUSG00000019970 -1.9011901 7.168098 630.19507 3.991683e-19 8.027845e-16
I try to get them into the list of character vectors, but have difficulty converting them and get the same errors. My geneIDs are of the form ENSMUSG00000026596. Could that be causing my error?
I have followed other entries on the help forum to figure it out without any resolution. I'm fairly new to R and definitely new to this type of analysis; so, any help is greatly appreciated.
Thank you for your time, Adelyn
Finally got it to work! (seems that once you ask for help, you always figure it out)
My issue must have been in the ensembl IDs I adapted the code from the manual 4.1.3 and got the feature to run.
Here is that code for ensembl ID to EntrezIDs for a mouse genome:
It just took me a few reads through until I got it! Hope this comment helps if other people are struggling like I did. Thanks Bioconductors for writing such a thorough manual and an awesome program!!!