similar to: Redirect standard input and output of R

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(),

Dear R-Help, I am using the function "topTable" from the LIMMA package. To estimate adjusted P-values there are several options (adjust="fdr" , adjust="BH") as shown below: topTable(fit, number = 10, adjust = "BH", fit$Name) I guess any of these options (fdr, BH, etc.) is using a default of FDR=0.05 which is quite conservative (i.e., very

I am getting the following error in my script. I am very very new to R and have obtained this script from another person. #read file in (dummy data) starburst.plot<-function(affy.fold, affy.FDR)(ifelse( ((affy.fold) >=0), -1*log10(affy.FDR), 1*log10(affy.FDR))) starburst.plot<-function(meth.fold, meth.FDR)(ifelse( ((meth.fold) >=0), -1*log10(meth.FDR), 1*log10(affy.FDR))) At my next

Hi all! I am intrested in the following scheme My mobile phone -> SMS to SOMETHING -> Redirect to FWD number -> FDW redirect to my * -> My * doing smtg There are companies like calluk.com that provide DIDs for free, but they do not support SMS. In http://www.voip-info.org/wiki-Asterisk+cmd+Sms they say "Works to ETSI ES 201 912 compatible with BT SMS PSTN service in UK"

I try to send this message To Gordon Smyth at smyth at vehi,edu.au but it bounced back, so here it is to r-help I am trying to use limma, just downloaded it from CRAN. I use R 2.0.1 on Win XP see the following: > library(RODBC) > chan1 <- odbcConnectExcel("D:/Data/mgc/Chips/Chips4.xls") > dd <- sqlFetch(chan1,"Raw") # all data 12000 > # > nzw <-

Dear All, It is not a typical R question (though I use R for this) but I thought someone will help me. For the list of P values, I have calculated FDR using p.adjust() in R (bioconductor). But my FDR values are same for all the P values. When do we get same FDR values? Does the smallest P values should less than 1/N? (where N is the number of P values) Thanks in advance. Kind regards, Ezhil

On 11/02/2017 01:42 PM, Fred Smith wrote: > I'm looking to replace my (old, creaky) netbook (Acer Aspire One D255e, > a screaming dual core 1.6 GHz Atom, and a whole 2 gigs of RAM) with > something faster but not too large. Sometimes (usually) the netbook is > painfully slow. > > Something like a hi-res 14 (or 15) inch screen (full HD), minimum of 4 gigs > RAM, HD of a

I have existing systems with un-encrypted disks. I have tried unsuccessfully to encrypt them using LUKS. Has anyone out there been able to encrypt an existing system (after the fact, so to speak)? TIA -- Roger Wells, P.E. leidos 221 Third St Newport, RI 02840 401-847-4210 (voice) 401-849-1585 (fax) roger.k.wells at leidos.com

On Wed, Mar 8, 2017 at 2:28 PM Tim Shen <timshen at google.com> wrote: > On Wed, Mar 8, 2017 at 1:49 PM David Blaikie <dblaikie at gmail.com> wrote: > > So I stumbled across an issue that I think is a bit fundamental: > > The xray runtime uses the C++ standard library. > > This seems like a problem because whatever C++ standard library is used to > compile the

Hello, I've a question about the fdr method in p.adjust: What is the threshold of the FDR, and is it possible to change this threshold? As I understand the FDR (please correct) it adjusts the p-values so that for less than N% (say the cutoff is 25%) of the alternative hypothesis the Null is in fact true. thanks a lot for help, +regards, Arne

I have developed a problem with the postscript output of plot on Windows. My code still works properly with R 2.3 but, with R 2.4, the white text on red background does not show up. It does, however, show up when output is sent to the screen. Below is my code and sessionInfo. R version 2.4.0 Under development (unstable) (2006-08-29 r39012) i386-pc-mingw32 locale: LC_COLLATE=English_United

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"

Dear R users, I am wondering about the following results: > p.adjust(c(0.05,0.05,0.05),"fdr") [1] 0.05 0.05 0.05 > p.adjust(c(0.05,0.04,0.03),"fdr") [1] 0.05 0.05 0.05 Why does p.adjust(..., "fdr") not adjust p-values, if they are constant? Does somebody have an explanation or can point to a reference? Thanks in advance, Will

> Note that "stripe" is not tested much and practically unmaintained. Ah, this was what I suspected. Understood. I'll be happy with "shard". Having said that, "stripe" works fine with transport=tcp. The failure reproduces with just 2 RDMA servers (with InfiniBand), one of those acts also as a client. I looked into logs. I paste lengthy logs below with

On Wed, Aug 16, 2017 at 4:44 PM, Hatazaki, Takao <takao.hatazaki at hpe.com> wrote: >> Note that "stripe" is not tested much and practically unmaintained. > > Ah, this was what I suspected. Understood. I'll be happy with "shard". > > Having said that, "stripe" works fine with transport=tcp. The failure reproduces with just 2 RDMA servers

Dear All, I'm classifying some data with various methods (binary classification). I'm interpreting the results via a confusion matrix from which I calculate the sensitifity and the fdr. The classifiers are trained on 575 data points and my test set has 50 data points. I'd like to calculate p-values for obtaining <=fdr and >=sensitifity for each classifier. I was thinking about

On Sun, Mar 12, 2017, 4:10 PM Dean Michael Berris <dean.berris at gmail.com> wrote: > > > On 9 Mar 2017, at 09:32, David Blaikie via llvm-dev < > llvm-dev at lists.llvm.org> wrote: > > > > I agree that we should clean up the standard library usage even just for > consistency. > > > > +1 -- now that I think about it, it should be fairly doable

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

Dear All: Significance Analysis of Microarrays(SAM) As we know sam do multiple t.test as following ## Default S3 method: t.test(x, y = NULL, alternative = c("two.sided", "less", "greater"),mu = 0, paired = FALSE, var.equal = FALSE,conf.level = 0.95, ...) var.equal: a logical variable indicating whether to treat the two variances as being equal. If 'TRUE'