search for: fdr

...9;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(), and which explains quite clearly the concept of an adjusted p-value. The idea that you're having trouble with actually has nothing specifically to do with FDR or with B&H's (1995) method. Any adjustment method for multiple testing can be expressed in terms of adjusted p-values. The function p.adjust() actually implements several adjustment methods, not just B&H's, where were not expressed in terms of p-values in their original papers....

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...

...re 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 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 Benj...

...re 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 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 Benj...

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 likely none of the tested genes will be ranked as differentiall...

I am using Efron's local fdr procedure. But, I want to change the null from N(0,1) to N(0, 0.002). I can access the function but I have no idea what to change. In other words, I want nulltype to be N(0,0.002) instead of N(0,1) in his function. Anyone has any ideas. This is his code for the local fdr: function (zz, bre = 120,...

Hello, I am initializing FDR mode and finalizing/flushing the buffers manually. XRay does not log calls from the main thread unless there is a function call after __xray_log_finalize(). This behavior is abnormal since one would expect the trace file to contain all function calls made up to the point when __xray_log_finalize()...

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 command, I get the following error: > g.ex.affy <- starburst.plot(data(,"affy.FOLD&qu...

Hola a todos, Tengo un pequeño problemilla... Tengo unas 9000 variables que he contrastado con 1 en concreto con el test de wilcoxon. He calculado el p-valor, y queria corregirlo con el permutation-based FDR. He encontrado una funcion con R comp.fdr()que hace esta corrección, pero te pide que le pongas las variables con las observaciones y te hace el test (según he entendido). Yo solo quiero que me calcule los q-valor. Sabeis como hacerlo? Muchas gracias Dolors [[alternative HTML version deleted]]

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, +re...

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

Dear List, We are planning a genotyping study to be analyzed using false discovery rates (FDRs) (See Storey and Tibshirani PNAS 2003; 100:9440-5). I am interested in learning if there is any consensus as to how many features (ie. how many P values) need to be studied before reasonably reliable FDRs can be derived. Does anyone know of a citation where this is discussed? Bill Dupont Will...

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

...bind(dd$AKR1C,dd$AKR2C,dd$AKR3C,dd$AKR1T,dd$AKR2T,dd$AKR3T) > bas <- cbind(dd$NZW1C,dd$NZW2C,dd$NZW3C,dd$AKR1C,dd$AKR2C,dd$AKR3C) > # > design<-matrix(c(1,1,1,1,1,1,0,0,0,1,1,1),ncol=2) > fit1 <- lmFit(nzw,design) > fit1 <- eBayes(fit1) > topTable(fit1,adjust="fdr",number=5) M t P.Value B 12222 3679.480 121.24612 7.828493e-06 -4.508864 1903 3012.405 118.32859 7.828493e-06 -4.508866 9068 1850.232 92.70893 1.178902e-05 -4.508889 10635 2843.534 91.99336 1.178902e-05 -4.508890 561 18727.858 90.17085 1.178902e-05...

...of writing anything to R. This program really works with the 'cat?? UNIX command, but it does not work with R. What I??m doing wrong??? It is possible to do it??? I want to start R once and use it thousands of times... that??s why I??m trying to use this system. pipe(fdW); pipe(fdR); pid = fork(); if (pid==-1) perror("Error fork"); if (pid==0) { close(0); dup(fdW[0]); close(fdW[0]); close(fdW[1]); close(1); dup(fdR[1]); close(fdR[1]); close(fdR[0]); execlp("R","R","--slave",NULL); perror("Error ex...

...of writing anything to R. This program really works with the 'cat?? UNIX command, but it does not work with R. What I??m doing wrong??? It is possible to do it??? I want to start R once and use it thousands of times... that??s why I??m trying to use this system. pipe(fdW); pipe(fdR); pid = fork(); if (pid==-1) perror("Error fork"); if (pid==0) { close(0); dup(fdW[0]); close(fdW[0]); close(fdW[1]); close(1); dup(fdR[1]); close(fdR[1]); close(fdR[0]); execlp("R","R","--slave",NULL); perror("Error ex...

Hello, Also, I’ve noticed that FDR mode doesn’t flush to a log unless programmatically configured to do so unlike basic mode, which flushes by default. Would it be possible to add this feature as well? Thanks, Henry -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.llvm.org/pipermai...

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....

...mpiler_rt_test(XRayUnitTests ${testname} 45 OBJECTS ${TEST_OBJECTS} 46 DEPS ${TEST_DEPS} 47 LINK_FLAGS ${TARGET_LINK_FLAGS} 48 -lstdc++ -lm ${CMAKE_THREAD_LIBS_INIT} 49 -lpthread 50 -L${COMPILER_RT_LIBRARY_OUTPUT_DIR} -lclang_rt.xray-fdr-${arch}) 51 endif()

...nted 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" "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 "conserv...