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Question: Problem testing qvalue 2.0.0
0
gravatar for tillea
2.3 years ago by
tillea0
Germany
tillea0 wrote:

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.

 

ADD COMMENTlink modified 2.3 years ago by Storey, John D.50 • written 2.3 years ago by tillea0

(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 REPLYlink modified 2.3 years ago • written 2.3 years ago by Dan Tenenbaum ♦♦ 8.2k

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 REPLYlink modified 2.3 years ago • written 2.3 years ago by tillea0
1
gravatar for Martin Morgan
2.3 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

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 COMMENTlink modified 2.3 years ago • written 2.3 years ago by Martin Morgan ♦♦ 20k

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 REPLYlink written 2.3 years ago by tillea0

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 REPLYlink written 2.3 years ago by Storey, John D.50
1
gravatar for Storey, John D.
2.3 years ago by
United States
Storey, John D.50 wrote:

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 COMMENTlink modified 2.3 years ago • written 2.3 years ago by Storey, John D.50
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