User: Storey, John D.

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Posts by Storey, John D.

<prev • 9 results • page 1 of 1 • next >
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Answer: A: qvalues lower than pvalues
... You're correct that q-values will eventually be smaller than p-values when pi0 < 1.  See: https://github.com/StoreyLab/qvalue#frequently-asked-questions There are finite sample results (meaning even for a small number of p-values) that show when the q-value estimates are conservative in Storey, ...
written 4 months ago by Storey, John D.50
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Answer: A: Q value obtained from QValue package is lower than P value?
... It's a red flag that your largest p-value 0.795.  The assumption is that true null p-values are Uniform(0,1), so the largest p-value should be close to 1 when this assumption is met and there are a reasonable number of tests being performed. From FAQ #1 (https://github.com/StoreyLab/qvalue/blob/mas ...
written 10 months ago by Storey, John D.50
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Answer: A: Error in dyn.load(file, DLLpath = DLLpath, ...) :
... Your error indicates there is a problem with the stringi package, which is not used by the qvalue package. ...
written 19 months ago by Storey, John D.50
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Comment: C: Problem testing qvalue 2.0.0
... 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. ...
written 2.3 years ago by Storey, John D.50
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Answer: A: Problem testing qvalue 2.0.0
... 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)   ...
written 2.3 years ago by Storey, John D.50
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Answer: A: How to use q.value cutt off in "decideTests" function for RNAseq differential ex
... I'm not the author of decideTests, so I'm not sure what it does.  However, qvalue can be used to determine significance cut-offs once p-values are obtained using the qvalue functions as demonstrated in the qvalue package's vignette.  With regards to q-values sometimes being smaller than p-values, th ...
written 2.4 years ago by Storey, John D.50
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Answer: A: Citations for TRIGGER
... trigger is based on these two papers: http://genomebiology.com/2007/8/10/R219 http://bioinformatics.oxfordjournals.org/content/24/19/2260.full     ...
written 2.7 years ago by Storey, John D.50
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Answer: A: Package qvalue - can it be installed without TCL-TK support?
... qvalue version 1.43.0 and all subsequent versions will not longer use tcltk. For those interested, a point-and-click Shiny version of qvalue is available here:  http://qvalue.princeton.edu/   ...
written 2.7 years ago by Storey, John D.50
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Comment: C: Package qvalue - can it be installed without TCL-TK support?
... We’re also about to release a version 2.x of qvalue that includes new functionality and resolves this issue. The temporary fix is okay with me. John From: Martin Morgan mtmorgan@fhcrc.org Reply: Martin Morgan mtmorgan@fhcrc.org Date: May 26, 2014 at 1:24:24 PM To: Giuseppe Gallone giuseppe.gall ...
written 3.5 years ago by Storey, John D.50

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