similar to: p.adjust; n > length(p) (PR#13519)

Full_Name: Ludo Pagie Version: 2.10.0 OS: linux, ubuntu, 8.04 Submission from: (NULL) (83.163.218.221) when I make a polygon with 100,000 vertices my X-server is being killed. This occurs in R-2.9.0 and a freshly installed R-2.10.0 I'm running Ubuntu with a locally compiled R: uname -a Linux onyx 2.6.24-24-generic #1 SMP Tue Aug 18 16:22:17 UTC 2009 x86_64 GNU/Linux xlower = -2e6:2e6

Hi all, I'm struggling a bit to get pgfSweave to lazyload objects when compiling a .Rnw file for a second time. Caching works fine except that for every run all objects get cached again and again. I've used cacheSweave which works fine; all cached objects from code-chunks with option cache = TRUE are lazy loaded. I've tried it on two machines ... I'm pretty sure I'm

Hi all, there appears to be something strange with the plotting of tables of 1 dimension; if I attempt to make a plot of a table of characters with only 1 value I get an error (Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' and 'y' lengths differ). With more than one value I don't get errors, neither with integers (even if only 1 value): tbl.char1 <-

Hi all, there appears to be something strange with the plotting of tables of 1 dimension; if I attempt to make a plot of a table of characters with only 1 value I get an error (Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' and 'y' lengths differ). With more than one value I don't get errors, neither with integers (even if only 1 value): tbl.char1 <-

Hi all, when I make a polygon with 100,000 vertices my X-server is being killed. This occurs in R-2.9.0 and a freshly installed R-2.10.0 I'm running Ubuntu with a locally compiled R: uname -a Linux onyx 2.6.24-24-generic #1 SMP Tue Aug 18 16:22:17 UTC 2009 x86_64 GNU/Linux xlower = -2e6:2e6 xupper = rev(xlower) ylower = runif(length(xlower)) yupper = ylower+.1

Hi- Is anyone working on multiple comparisons of means or post-hoc tests (ie: Tukey, Bonferroni) for R? I saw in the winter 98' archives of the R mailing lists that these tests had not been implemented yet, I was just wondering if I could look foward to having them. ;-) I also looked through the contributed packages and didn't see anything that offered such tests. I guess I could check

Matt, Here's a Bonferroni-corrected multiple one-sample t-test that I wrote some years ago. It took a while to get it into R, as na.omit doesn't seem to handle vectors and I had to write a quick kludge (na.remove). Another more general point was that I discovered that the help page for t.test gives the name "parameters" for the degrees of freedom, as in S. However, the name

20 subjects were measured in 5 conditions (thus repeated measures) and for each subject in each condition there are 4 response measures (thus multivariate as it is a combined score that needs to be compared across the conditions). So, using a multivariate approach to repeated measures this is a doubly multivariate analysis. I would appreciate any suggestions as to the best way to do such a

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"

Hi, I have a box with XEN enabled. Specs : Gentoo 10.0 AMD64 XEN 4.0.0 The server is connected on our network through two physicals NIC. Actually, I''m using a VLAN on each NIC and bridge the domU in it. But now I must create an additional domU which should be in an different VLAN. The best solution is to set a trunk on the switch and use 802.1q directly on the dom0. I found this site

Hi, I have two questions want to ask. 1. If I have a matrix like this, and I want to figure out the rows whose value in the 3rd column are less than 0.05. How can I do it with R. hsa-let-7a--MBTD1 0.528239197 2.41E-05 hsa-let-7a--APOBEC1 0.507869409 5.51E-05 hsa-let-7a--PAPOLA 0.470451884 0.000221774 hsa-let-7a--NF2 0.469280186 0.000231065 hsa-let-7a--SLC17A5

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

Hello Valery, I have some comments regarding your thoughts on LLVM support for distributed computing. Valery A.Khamenya wrote: >There should be an engine and layer for making dispatching optimizations in run-time. If one CPU is loaded and code is >"parallelizable" why then not to send some part of >calculation to other CPU? This kind of on-fly decision will >be one day

> dim(data.sub) [1] 10000 140 #####extracting all differentially express genes########## library(multtest) two_side<- (1-pt(abs(data.sub),50))*2 diff<- mt.rawp2adjp(two_side) all_differ<-diff[[1]][37211:10000,] all_differ #####list of differentially expressed genes########## > probe.names<- + all_differ[[2]][all_differ[[1]][,"BY"]<=0.01] Error in

Hello, I've fitted a parametric survival model by > survreg(Surv(Week, Cens) ~ C(Treatment, srmod.contr), > data = poll.surv.wo3) where srmod.contr is the following matrix of contrasts: prep auto poll self home [1,] 1 1 1.0000000 0.0 0 [2,] -1 0 0.0000000 0.0 0 [3,] 0 -1 0.0000000 0.0 0 [4,] 0 0 -0.3333333 1.0 0 [5,] 0 0

hi list, i have to ask you again, having tried and searched for several days... i want to do a TukeyHSD after an Anova, and want to get the adjusted p-values after the Tukey Correction. i found the p.adjust function, but it can only correct for "holm", "hochberg", bonferroni", but not "Tukey". Is it not possbile to get adjusted p-values after

Hello, I have 3 hdd (120 GB, 120 GB and 80 GB) mounted on /data1 , /data2 and /data3. All these drives must be shared via a public access with Samba. For the moment, I can only share the 'data1' directory. [public] path = /data1 Is there a possibility to share several disks under the same account ? By example : [public] path = /data1, /data2, /data3 Then, under Windows, I'd like

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

Hi ! I wanted to shape my analog modem connection so I took these two lines from the ''wondershaper'' script: tc qdisc add dev $DEV handle ffff: ingress #tc filter add dev $DEV parent ffff: protocol ip prio 50 u32 match ip \ src 0.0.0.0/0 police rate ${DOWNLINK} burst 10k drop flowid :1 with DEV=ppp0 and DOWNLINK=24kbit. But, when I activate it, nothing comes back from the

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