search for: benjamini

...ods that R has? Is there any particular advantage to the Dunn-Sidak method? R knows about these methods (in R 2.1.1): > p.adjust.methods [1] "holm" "hochberg" "hommel" "bonferroni" "BH" "BY" "fdr" [8] "none" BH is Benjamini & Hochberg (1995) and is also called "fdr" (I wish R's documentation said this clearly). BY is Benjamini & Yekutieli (2001). I found a few hits from Google on Dunn-Sidak, but I'm curious if anyone can tell me on a "conservative-liberal" scale, where the Dunn-Si...

L.S. In the current version of ?p.adjust.Rd, one needs to scroll down to the examples section to find confirmation of one's guess that "fdr" is an alias of "BH". Please find a patch in attachment which mentions this explicitly. Best, Tobias -------------- next part -------------- A non-text attachment was scrubbed... Name: p.adjust.Rd.patch Type: text/x-patch Size: 633

Dear R contributors, I suggest adding a new method to `p.adjust` ("Adjust P-values for Multiple Comparisons", https://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html). This new method is published in Benjamini, Krieger, Yekutieli 2016 Adaptive linear step-up procedures that control the false discovery rate (Biometrika). https://doi.org/10.1093/biomet/93.3.491 This paper described multiple methods for adjusting p-values, where the "TST" method (Definition 6) performed the best when test statist...

...gt; misunderstandings or confusions regarding across which tests the FDR > "correction" is being applied. My question is more fundamental and > involves how the FDR method is implemented at the level of "p.adjust" > (package: stats). > > I have reread the paper by Benjamini and Hochberg (1995) and nowhere in > their paper do they actually "adjust" p values; rather, they develop > criteria by which an appropriate p value maximum is chosen such that FDR > is expected to be below a certain threshold. > > To try to get a better handle on this, I w...

In The American Statistician vol 42 (1988) pages 257 - 280, Yoav Benjamini investigates some variations on the box plot, including vaseplots, which maek the width of each box vary proportionally to he estimated density at a particular point. Has anyone implemented these in R ? Thanks as always Peter

Mark, there is a fdr website link via Yoav Benjamini's homepage which is: http://www.math.tau.ac.il/%7Eroee/index.htm On it you can download an S-Plus function (under the downloads link) which calculates the false discovery rate threshold alpha level using stepup, stepdown, dependence methods etc. Some changes are required to the plotting code w...

...FDR. Some of them involved misunderstandings or confusions regarding across which tests the FDR "correction" is being applied. My question is more fundamental and involves how the FDR method is implemented at the level of "p.adjust" (package: stats). I have reread the paper by Benjamini and Hochberg (1995) and nowhere in their paper do they actually "adjust" p values; rather, they develop criteria by which an appropriate p value maximum is chosen such that FDR is expected to be below a certain threshold. To try to get a better handle on this, I wrote the following simp...

...FDR. Some of them involved misunderstandings or confusions regarding across which tests the FDR "correction" is being applied. My question is more fundamental and involves how the FDR method is implemented at the level of "p.adjust" (package: stats). I have reread the paper by Benjamini and Hochberg (1995) and nowhere in their paper do they actually "adjust" p values; rather, they develop criteria by which an appropriate p value maximum is chosen such that FDR is expected to be below a certain threshold. To try to get a better handle on this, I wrote the following simp...

...-miR-205--SERPINB5 0.744124886 3.28E-11 hsa-miR-205--PBX1 0.734487224 7.89E-11 hsa-miR-205--MCC 0.72499934 1.80E-10 hsa-miR-205--WNT5B 0.717705259 3.33E-10 hsa-miR-200c--PKN2 0.721746815 3.46E-10 hsa-miR-200c--PCYOX1 0.721698034 3.48E-10 hsa-miR-200c--WDR68 0.72068017 3.78E-10 And I want to do the Benjamini & Hochberg correction. So I run : rm(list=ls()) a<-read.csv("1-correlation.txt",sep="\t",header=F,quote="") c<-p.adjust(a$V3,"BH") a[,4]<-c write.table(a,"zz.txt",sep="\t") And I got the result: hsa-miR-205--GATA3 0.797882...

Hello, I am not sure about the p.adjust( , fdr). How do these adjusted p-values get? I have read papers of BH method. For independent case, we compare the ordered p-values with the alfa*i/m, where m is the number of tests. But I have checked that result based on the adjusted p-values is different with that by using the independent case method. Then how do the result of p.adjust( , fdr) come? And

I append below a suggested update for p.adjust(). 1. A new method "yh" for control of FDR is included which is valid for any dependency structure. Reference is Benjamini, Y., and Yekutieli, D. (2001). The control of the false discovery rate in multiple testing under dependency. Annals of Statistics 29, 1165-1188. 2. I've re-named the "fdr" method to "bh" but kept "fdr" as a synonym for backward compatability. 3. Upper case val...

...c compo- nents (e.g., the output of split'). Missing values (NAs) are allowed. type=: character string (the first letter suffices) specifying type of gboxplots, currently "box" for Tukey's boxplots, "vase" for vase or violin plots (see Benjamini (1988) and Hintze and Nelson (1998)), "diamond" for diamond plots (see, for instance, JMP (1995)), or "pts" for one dimen- sional histograms (See Chambers et. al. (1983)). Type may also be the name of a user-written function that computes...

dear all, I recently came across the following issue and I was not sure whether it is intentionally or not: using p.adjust to adjust p-values for multiple hypothesis testing using the method from Benjamini and Hochberg removes all NA values from the input vector and does not account for them in the adjustment, i.e. in a vector of 23 p-values with 20 of them being NA it adjusts the 3 non-NA p-values as if there had only been 3 tests to adjust for (see example). I was not aware of that behaviour, and a...

...annotation categories. I think that for the case of Bonferroni corrections, I should correct this output by the total number of possible tests conducted (3121): >phyper(26,830,31042,337, lower.tail=F)*3121 >phyper(16,387,31042,337, lower.tail=F)*3121 But I would like to perform FDR, i.e. Benjamini correction. I know that multtest package has the function mt.rawp2adjp() but I would need to save all the p.values for the 3121 in a vector and use this as a parameter of the function. Is there another way of computing this adjusted p.value for only some of the categories? Thanks for your hel...

...blem with the function "p.adjust" in stats. I have looked at the manuals and searched the R site, but didn't get anything that seems directly relevant. Can anybody throw any light on it or confirm my suspicion that this might be a bug? I am trying to use the p.adjust() function to do Benjamini/Hochberg FDR control on a vector of p-values that are the smallest K p-values selected from an N-length vector. So I am using p.adjust(p, n=N, method="BH") This seems to give smaller adjusted p-values than if I use p.adjust(p, method="BH"). For example (K=10, N=20) > p=runi...

Benjamin Ylvisaker <benjaminy at alumni.cmu.edu> writes: > I am interested in working on a little architecture project that > involves modifying an ISA in some non-trivial ways and seeing what > impact it has on instruction frequencies (and other such metrics). > Clearly I'll need to hack on a compiler backend, and I thought that > LLVM might be a good choice

I am interested in working on a little architecture project that involves modifying an ISA in some non-trivial ways and seeing what impact it has on instruction frequencies (and other such metrics). Clearly I'll need to hack on a compiler backend, and I thought that LLVM might be a good choice since among mature compiler infrastructures it's fairly young and presumably

...each p-values from 0.0001 to 0.05 So that I can use a good cutoff as significance level (alpha) to exclude the gene profiles which are weakly associated with all expression profiles. (If I am correct, to do this I need to use other p-value correction methods, either simulation based, resampling or Benjamini and Hochberg (B&H). Please can any one suuggests me about p-value adjustment or p-value correction, I mean statistically or technically which number should I consider for correction, 10340 or 3 * 10340, as I have three features to associate with same 10340 gene set. or if I am wrong, can any o...

On Jun 9, 2011, at 8:09 PM, David A. Greene wrote: > Note that things like instruction frequencies are highly ISA- > dependent. If possible, it is best to evaluate your ideas on more > than one target, just to see what the effects are. What other sorts > of things do you want to study? > > If, long-term, you are planning to do serious studies of performance >