User: Storey, John D.

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Posts by Storey, John D.

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Answer: A: EDGE: Persistent lrt() and odp() command pi0est() error due to low p values
... Since you have so few tests, I recommend using the lrt() function instead of odp() which will simply performs a t-test or F-test.  All you need to do is add lambda=0 as an argument and it will be passed to qvalue(): lrt(de_obj_TimeSeries, lambda=0) Setting lambda=0 yields the Benjamini-Hochberg ...
written 7 months ago by Storey, John D.60
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Comment: C: EDGE: Persistent lrt() and odp() command pi0est() error due to low p values
... Since you have so few tests, I recommend using the lrt() function instead of odp() which will simply performs a t-test or F-test.  All you need to do is add lambda=0 as an argument and it will be passed to qvalue(): lrt(de_obj_TimeSeries, lambda=0) Setting lambda=0 yields the Benjamini-Hochberg e ...
written 7 months ago by Storey, John D.60
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Answer: A: qvalue package throws error when used on any p-values but hedenfalk example
... You don't have enough p-values to warrant estimating pi0, so include the argument lambda=0. ...
written 7 months ago by Storey, John D.60
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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 14 months ago by Storey, John D.60
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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 20 months ago by Storey, John D.60
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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 2.4 years ago by Storey, John D.60
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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 3.2 years ago by Storey, John D.60
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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 3.2 years ago by Storey, John D.60
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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 3.3 years ago by Storey, John D.60
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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 3.5 years ago by Storey, John D.60

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