EdgeR Error: could not find function "glmQLFit"

[susanklein]

Hi,

anyone know why I get this error trying to use edgeR? I installed everything according to https://bioconductor.org/packages/re...tml/edgeR.html but when I try out the example at https://bioconductor.org/packages/re...UsersGuide.pdf I get the error:

> fit <- glmQLFit(y,design)
Error: could not find function "glmQLFit"

I'm a complete newbie to R so sorry if I missed something obvious.

Thanks for any help.. can't find this issue anywhere.

S.

[wdecoster]

Just to be sure, but did you, after installation of edgeR, also import it?
library("edgeR")

[susanklein]

ah, yes, that was it, thanks!!

[susanklein]

actually.. it wasn't it.. I just tried it out and still getting

> fit <- glmQLFit(y,design)
Error: could not find function "glmQLFit"


? anyone?

Thanks

S.

[wdecoster]

You have to load the library every time you start a new R session.

[susanklein]

yes, done that.

[wdecoster]

Could you give me the output of the following function (in R)?
sessionInfo()

[susanklein]

...sorry have to wait 5 mins to reply (when did that rule come in?)...

> 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] BiocInstaller_1.14.3 locfit_1.5-9.1 edgeR_3.6.8
[4] limma_3.20.8

loaded via a namespace (and not attached):
[1] grid_3.1.1 lattice_0.20-29 tools_3.1.1

[wdecoster]

Based on that, you have edgeR version 3.6.8.

I would like to point you to this: https://bioconductor.org/packages/re...ews/edgeR/NEWS
(you can get there from the bioconductor page of edgeR)
which will tell you everything what is new in which version, including the following:

Changes in version 3.8.0:
o glmQLFTest() is split into three functions: glmQLFit() for fitting
quasi-likelihood GLMs, glmQLFTest() for performing quasi-likelihood
F-tests and plotQLDisp() for plotting quasi-likelihood dispersions.

I think that glmQLFit indeed doesn't exist in your edgeR version and updating edgeR will fix that...

[susanklein]

But that's absurd!? I followed the installation instructions on the Bioconductor site:

https://bioconductor.org/packages/release/bioc/html/edgeR.html

source("http://bioconductor.org/biocLite.R")
biocLite("edgeR")

then used the quick start in the latest manual:

https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf

so the manual is correct but the edgeR version on the Bioconductor page is wrong?

so how do I update edgeR?

Thanks.

S.

[susanklein]

is this because my version of R is too old perhaps?

[wdecoster]

I just installed edgeR on another machine to check, and I get version 3.12.1. You could indeed try to update R, which is fairly outdated.

(version problems is one of the things I really don't like about R)

[susanklein]

Thanks, I'll try that. It does work in the windows version of R so for now I'm just using that. Updating R (as a module) in my debian machine is not straightforward..

S.