Question

voomWithQualityWeights not functioning - function not found

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harelarik ▴ 60

@harelarik-13564

Last seen 3.1 years ago

Israel

Hi,

I can not seem to make voomWithQualityWeights work.

Could you please help me?

1. LIMMA is installed (see version below) and help command for voomWithQualityWeights() works but the function is not found by R:

>voomWithQualityWeights()

Error in voomWithQualityWeights() :

could not find function "voomWithQualityWeights"

#x is a DGEList object generated by LIMMA, which was used to generate lmFit and voom object

>voomWithQualityWeights(x$counts,design=des)

Error in voomWithQualityWeights() :

could not find function "voomWithQualityWeights"

>voomWithQualityWeights(x,design=des)

Error in voomWithQualityWeights() :

could not find function "voomWithQualityWeights"

2. Installed versions:

> sessionInfo()

R version 3.4.1 (2017-06-30)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu 14.04.5 LTS

other attached packages:

[1] BiocInstaller_1.26.0 RColorBrewer_1.1-2 edgeR_3.18.1

[4] limma_3.32.5

3. Help command is working for voomWithQualityWeights:

?voomWithQualityWeights is working showing help page

help(voomWithQualityWeights) is working showing help page

Thank you very much,

Arik

limma • 2.1k views

ADD COMMENT • link 7.3 years ago harelarik ▴ 60

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#The following commands are working for the x DGEList object (x) and for the design (des):

v <- voom(x, des, plot=TRUE)

vfit <- lmFit(v, design)
vfit <- contrasts.fit(vfit, contrasts=contrast.matrix)
efit <- eBayes(vfit)
plotSA(efit)

ADD REPLY • link 7.3 years ago harelarik ▴ 60

score 0 · Answer 1 · 2017-08-03

Well, it's hard to give you any help because I can't think of any circumstances in which what you say would be possible. As far I as I know, it's not possible to have limma attached but for voomWithQualityWeights() to not be found.

Even if the function voomWithQualityWeights() didn't exist in your search path, the error message would not be the same as shown in your post. The error message confirms that the voomWithQualityWeights function has in fact been run (otherwise the error couldn't emanate from "in" the function) but then it says it can't find the same function.

Furthermore,the error message says that voomWithQualityWeights() has been run without any arguments, but there is no such code anywhere in the limma package.

Sorry, but none of this makes sense to me.

score 0 · Answer 2 · 2017-08-03

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harelarik ▴ 60

@harelarik-13564

Last seen 3.1 years ago

Israel

What can I do??

ADD COMMENT • link 7.3 years ago harelarik ▴ 60

1

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My guess is that you have a second definition of voomWithQualityWeights() in your environment, maybe from working with devtools or ??? You could try to resolve the function explicitly limma::voomWithQualityWeights(). Also use R from the command line and start with R --vanilla so that your session does not contain objects from previous sessions / things you might be doing in your .Rprofile, etc.

ADD REPLY • link 7.3 years ago Martin Morgan 25k

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I thought about the possibility of a second definition of the voomWithQualityWeights before I wrote my own reply, but I can't think of any situation that would give the same error messages as reported.

ADD REPLY • link 7.3 years ago Gordon Smyth 51k

Gordon Smyth · Answer 3 · 2017-08-06

Thank you very much.

I suspect Martin is right.

It must be some command that overridden the voomWithQualityWeights()

I have terminated R session (ctrl+D).

Than started a new one.

Than:

>library(limma)
>library(edgeR)

> voomWithQualityWeights()
Error in is(counts, "DGEList") :
argument "counts" is missing, with no default

This is the a good sign. The function is recognized!

>expMatrixAll = read.csv("June2016_McapCDS_RNAseq_UniqueReads_CountMatrix_excludingLowCounts_thresh10.csv",header=TRUE)

>x<-DGEList(counts=expMatrixAll[, -c(1)], genes=data.frame(Length=geneLen))

Now:

>voomQWeights<-voomWithQualityWeights(x$counts)

Working!!

I do not know what was it that made voomWithQualityWeights() stop working (overridden?).

When I will find it, I will add it to this session.

Thank you very much again,

Arik