Another option would be to use the siggenes package which implements Storey's q-value calculation but doesn't have the tcl/tk dependency. I think this will work (but you should double-check to make sure it gives the expected result): library(siggenes) # pval is a vector of p-values pi0<-pi0.est(pval)$p0 qval<-qvalue.cal(pval, pi0) Martin. On Mon, Mar 8, 2010 at 1:07 PM, Guruprasad Ananda <gua110@bx.psu.edu> wrote:
Hi Zaky,
The warning message you are getting is not from the call to 'qvalue' function, but from the library call step. If you use suppressWarnings(library(qvalue)), the warning should disappear and your Galaxy output should turn green. Please give it a shot and let me know if it doesn't work.
Thanks, Guru.
On Mar 8, 2010, at 12:42 PM, Jeremy Goecks wrote:
Hi Zaky,
There are people on the galaxy-dev list (cc'd) that will be better able to assist you with this problem than me.
Best, J.
On Mar 8, 2010, at 12:11 PM, ZAKY ADAM wrote:
Hi Jeremy,
I am running a perl program that embeds some R commands. The R commands require a package called "qvalue". Running the R commands included in this package results in some graphics in PDF. The program works perfectly on my computer, but does not work on my galaxy that I have on scofield. I need this to run on scofield in order to complete my workflow.
The R commands are the following:
library(tcltk); library(qvalue); p <- scan("p_valuesInputFile.txt"); qobj <- qvalue(p, fdr.level = 0.05);
I am reading simply 104 p values (in statistics) and save them in the variable p, then the last command from the "qvalue" package should convert them into what is called q values, but requires a graphical device. This last line generates always the following error message:
Loading Tcl/Tk interface ... done Warning message: In fun(...) : no DISPLAY variable so TK is not available Read 104 items
You don't need to be concerned with the code itself because, as I said, it works perfectly on my mac os x computer. The problem is that Galaxy can not deal with this graphical issue. I hope that you can be helpful on this.
Zaky Adam Postdoctoral Research Fellow Center for Comparative Genomics and Bioinformatics The Pennsylvania State University 306 Wartik Lab University Park, PA 16802 (814) 863-2185 zua4@psu.edu
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Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University
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-- Post-doc Yegnasubramanian Lab / Irizarry Lab Johns Hopkins Schools of Medicine and Public Health