similar to: Suggestion for updating `p.adjust` with new method (BKY 2006)

The Partek package (www.partek.com) allows only two selections for Multiple Test Correction: Bonferroni and Dunn-Sidak. Can anyone suggest why Partek implemented Dunn-Sidak and not the other methods 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"

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

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

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

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

You asked the same question on the Bioconductor mailing list back in August. At that time, you suggested yourself a solution for how the adjusted p-values should be interpreted. I answered your query and told you that your interpretation was correct. So I'm not sure what more can be said, except that you should read the article Wright (1992), which is cited in the help entry for p.adjust(),

Hi! We found some problems with those patches, and ended up doing slightly different fix: https://github.com/dovecot/core/compare/3e41b3d%5E...cca98b.patch Aki On 24.10.2016 10:17, Aki Tuomi wrote: > Hi! > > Can you try these two patches? > > Aki > > > On 24.10.2016 08:48, Aki Tuomi wrote: >> Ok so that timeval makes no sense. We'll look into it. >>

Hi, There is a question that I am confused. I have a set of data like this: hsa-miR-205--GATA3 0.797882767 1.08E-13 hsa-miR-205--ITGB4 0.750217593 1.85E-11 hsa-miR-187--PGF 0.797604155 3.24E-11 hsa-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

seek(zz,where=NewPosition) returns the OldPosition of connection zz (of the appropriate "pointer", i.e. read or write). Currently, the docs have: > Details: > > `seek' with `where = NA' returns the current byte offset of a > connection (from the beginning), and with a positive `where' > argument the connection is re-positioned (if possible) to

Hi - I'm using Icecast to stream some audio that I embed in an <audio> tag on a webpage. This is working great for desktop browsers and on iOS, but it doesn't work on Android. It looks like Chrome mobile sends the header "Range: bytes=0-1" and then doesn't try to load any more data when Icecast responds with a 0 byte "HTTP/1.0 200 OK" response. From my

We have two lectureship positions advertised at the moment. One (or both) of these is intended for a specialist in statistical computation. The salary doesn't look great by international standards but there are compensations: housing is cheap, the air is clean, and the worlds problems are far away. We also have a track record of getting tenure for computing people.

I'd like to get summary statistics (really just a mean would be fine) for a vector in a data frame, but split based on the value of another vector. That is, I have a data frame (hcd.df) with variables datecat (which is always 1 or 2) and auth.sum (-8..+8). I've used xtabs to get chi-square comparisons, but what I need now is a simple mean of auth.sum where datecat is 1 and another where

In a recent post, I reported that help.start worked with Mozilla, although it had not worked before. I now have discovered the difference. I'm using RH Linux 7.1 and Mozilla 0.9.5 and R 1.3.1. When I tried it before, I had use ESS to start R. If I run R without ESS, help.start() will start the browser (Mozilla), but help(apply), for example, will produce help in ESS but not in the browser.

Probably wrong group for this, but a quick question. I've just switched from emacs to Xemacs. In reinstalling ESS 5.1.19 I keep getting the following error when loading Xemacs: "Error in init file: Symbol's function definition is void: w32-using-nt" I've debugged the ess-site.el file, which is where the error originates from. The line causing the difficulty is:

Hi, I?m a new Dovecot user and using version 2.2.18 on an OpenSuse system. In general it all works quite nicely and clients can connect to Dovecot and manage mails normally. The layout used is maildir. The users are all virtual, i.e. they do not exist on the Linux system. They all log in without any authentication due to a very specialized and internal setup. However, sometimes Dovecot simply

On RedHat linux 7.2, I upgraded (?) Emacs and R at the same time and now I'm getting some funny business with R and ESS. I reinstalled ESS from the tarball and re-byte-compiled. In particular, help.start() does work, and ESS works to send text regions to the R process, but ?function does not return anything, and the status line says "ESS process not ready. Finish your command

I am posting this to both R and BioC communities because I believe there is a lot of confusion on this topic in both communities (having searched the mail archives of both) and I am hoping that someone will have information that can be shared with both communities. I have seen countless questions on the BioC list regarding limma (Bioconductor) and its calculation of FDR. Some of them involved

I am posting this to both R and BioC communities because I believe there is a lot of confusion on this topic in both communities (having searched the mail archives of both) and I am hoping that someone will have information that can be shared with both communities. I have seen countless questions on the BioC list regarding limma (Bioconductor) and its calculation of FDR. Some of them involved

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 when porting it to R. I removed the

that seems to fix this kevent() problem, but I got the following lucene assert. Is that because of previous fails? Also, while I have your attention, is fts_autoindex supposed to work accross NAMESPACES? doveadm(mrm): Debug: Mailbox LISTS/vse-l: Opened mail UID=39483 because: fts indexing doveadm(mrm): Debug: Mailbox LISTS/vse-l: Opened mail UID=39484 because: fts indexing doveadm(mrm): Debug: