Question

Problem testing qvalue 2.0.0

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tillea • 0

@tillea-8462

Last seen 9.7 years ago

Germany

Hi

I intend to upgrade the Debian package of qvalue and tried to test it by trying to reproduce vignettes/qvalue.Rnw but failed.

> library(qvalue)
> data(hedenfalk)
> length(hedenfalk)
[1] 3
> hist(hedenfalk)
Error in hist.default(hedenfalk) : 'x' must be numeric

Any hint what might be wrong here?

Kind regards

Andreas.

qvalue • 2.0k views

ADD COMMENT • link updated 9.7 years ago by Storey, John D. ▴ 100 • written 9.7 years ago by tillea • 0

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(I'm not the qvalue maintainer)

I was able to reproduce this with the devel version of Bioc (sessionInfo below). I got the following traceback afterwards:

3: stop("'x' must be numeric") 2: hist.default(hedenfalk) 1: hist(hedenfalk)

Turns out hedenfalk is a list.

It works if you say

hist.default(unlist(hedenfalk))

So maybe that's a clue for the qvalue maintainer.

> sessionInfo() R version 3.2.1 (2015-06-18) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux stretch/sid

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] qvalue_2.1.0 BiocInstaller_1.19.8

loaded via a namespace (and not attached): [1] Rcpp_0.11.6 digest_0.6.8 MASS_7.3-42 grid_3.2.1 [5] plyr_1.8.3 gtable_0.1.2 magrittr_1.5 scales_0.2.5 [9] ggplot2_1.0.1 stringi_0.5-5 reshape2_1.4.1 splines_3.2.1 [13] proto_0.3-10 tools_3.2.1 stringr_1.0.0 munsell_0.4.2 [17] colorspace_1.2-6 >

ADD REPLY • link 9.7 years ago Dan Tenenbaum ★ 8.2k

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I need to check things thorough. I noticed that I was working on an old vignettes file. May be I made some unneeded noise.

ADD REPLY • link 9.7 years ago tillea • 0

score 1 · Answer 1 · 2015-07-23

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Martin Morgan 25k

@martin-morgan-1513

Last seen 11 weeks ago

United States

Seems like the vignette doesn't do this, but hist(hedenfalk$p) or other commands. This is from the R script file associated with the vignette on the package landing page. This is also available in a correctly installed package via

fl = system.file(package="qvalue", "doc", "qvalue.R")
source(fl)

or from the source directory by

% cd qvalue/vignettes
% R CMD Stangle qvalue.Rmd
% R -f qvalue.R

ADD COMMENT • link 9.7 years ago Martin Morgan 25k

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I can confirm that

fl = system.file(package="qvalue", "doc", "qvalue.R")
source(fl)

I think I mixed up something and have used by accident an old version of the vignette. I need to dive deeper into this and may be I come back here (hopefully not).

Thanks for the hints

Andreas.

ADD REPLY • link 9.7 years ago tillea • 0

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Please don't hesitate to ask any additional questions if you have them. I recommend doing a clean installation of the latest version of qvalue from Bioconductor.

ADD REPLY • link 9.7 years ago Storey, John D. ▴ 100

score 1 · Answer 2 · 2015-07-23

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Storey, John D. ▴ 100

@storey-john-d-6576

Last seen 5.3 years ago

United States

The code you use above isn't in the current vignette. In version 2.0.0, the object hedenfalk is now a list. Try:

> library(qvalue)

> data(hedenfalk)

> ?hedenfalk

> names(hedenfalk)
[1] "p"     "stat"  "stat0"

> length(hedenfalk$p)
[1] 3170

> hist(hedenfalk$p)

ADD COMMENT • link 9.7 years ago Storey, John D. ▴ 100