Hi,

here's my lines, basically taken from the EdgeR manual. I always get this error.

> library("edgeR")

> x <- read.delim("counts",row.names="geneid")

> group <- factor(c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2))
> y <- DGEList(counts=x,group=group)
> y <- calcNormFactors(y)
> design <- model.matrix(~group)
> y <- estimateDisp(y,design)
Loading required package: splines
> fit <- glmQLFit(y,design)
Error: could not find function "glmQLFit"

Thanks for any help..

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] locfit_1.5-9.1 edgeR_3.6.8    limma_3.20.8

loaded via a namespace (and not attached):
[1] grid_3.1.1      lattice_0.20-29

In the older version of edgeR that you are using, you can simply call glmQLFTest() directly:

y <- estimateDisp(y,design)
results <- glmQLFTest(y, design)
topTags(results)

Please read the help page for that function. There is a case study in the User's Guide (the Nigerian samples) showing you how to run it. Of course you have to read the User's Guide that comes with your version of R rather than a User's Guide for a later version of R.

However updating R and edgeR to the latest would obviously be preferable.

I have found out, this is a problem with my version of R and it cannot download the latest edgeR, therefore the syntax for the function was wrong. I need to try updating R then updating edgeR.