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Commit new versions of test outputs for some tools that use R and generate PDFs. The outputs are effectively the same but the actual PDF code varies slightly thanks to a newer version of R. Also, suppress noise in the compute_q_values tool that was causing its test to fail.

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Nate Coraor
2010-09-28 17:05:36 -04:00
parent d3e5f3eda9
commit c09df6b5b2
1 changed files with 2 additions and 2 deletions
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tools/regVariation/compute_q_values.pl
+2 -2
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@@ -52,11 +52,11 @@ print Rcmd "
#options(show.error.messages = FALSE);
#load necessary packages
library(tcltk);
suppressPackageStartupMessages(library(tcltk));
library(qvalue);
#read the p-values of the multiple simultaneous tests from the input file $p_valuesInputFile
p <- scan(\"$p_valuesInputFile\");
p <- scan(\"$p_valuesInputFile\", quiet = TRUE);
#compute the q-values that correspond to the p-values of the multiple simultaneous tests
qobj <- qvalue(p, pi0.meth = \"$pi0_method\", lambda = $lambdaValue, fdr.level = $fdr_level, robust = $robustValue);