similar to: lmPerm p-values and multiple testing

I've found a problem when using categorical variables in lmp() from package lmPerm According to help(lmp): "This function will behave identically to lm() if the following parameters are set: perm="", seq=TRUE, center=FALSE.") But not in the case of including categorical variables: require(lmPerm) set.seed(42) testx1 <- rnorm(100,10,5) testx2 <-

Hi all, Dear Dr. Wheeler, I am trying to use the lmPerm package to perform multiple regression on microarray data with certain empirical variables associated with treatments of the experiment. In order the circumvent the very conservative multiple test corrections such as Bonferroni and BH, I try to use permutated probabilities to assess associations. In addition to mu previous posting I

Hello, useR:, Suppose I have two plots made by using contour() function, say Cont1 and Cont2 respectively. They have slightly difference because of the two slightly different data I used. I want to see the difference between them so I want to plot Cont2 on Cont1, are there any methods to plot it without filling the frame of Cont1 totally of Cont2. I mean, how I can integreate the two plots

Hi guys i found this encryption decryption in php and try to convert it in rails but i am unable to successfully convert it. So plz help me. I you write the whole conversion code then it will be great. PHP code is like this ================ # #/********************************************** #** #** MD5 block cypher #** #** Author..: leapinglangoor [

I get the following message on a Centos 5 system (really a Trixbox 2.4 build on Centos 5): Jan 14 00:12:28 sip2 kernel: hub 1-0:1.0: connect-debounce failed, port 1 disabled What does this mean? This message occurs about 30 times/sec for about 45 sec. Then my Bluetooth token starts up. Jan 14 00:12:28 sip2 kernel: hub 1-0:1.0: connect-debounce failed, port 1 disabled Jan 14 00:13:00 sip2

Hi there, the attached R function uses the SAS Integrated Object Model (IOM) and it can deal with SAS dates and long variable names. All you need to provide is the folder where the SAS data file is and the data file name without the extension. The function requires the rcom package. This is meant to be first cut...but improvements and suggestions are more than welcome! Gyula import.sas.data

Hi *, This is my first message to this list, so I hope I am not breaking any rule with my post. My question is the following: can I establish a voice connection over an ISDN interface by using a bluetooth dongle to connect to the ISDN access point? Here follow the details: I have compiled and configured asterisk. Everything seems fine except that when I configure asterisk to use the ISDN

Hi Reid, I've been working on the outlining code and have a prototype that produces what I want for a simple case. Now I'm thinking about the heuristics for recognizing the various logical pieces for C++ exception handling code and removing them once they’ve been cloned. I've been working from various comments you've made earlier in this thread, and I'd like to run something

Hi how can I find, in a vector of characters, which is the most frequent one? Thanks Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppolig at mail.nih.gov

Hi, I want to generate a number of vectors and store them with different names, like this: x=1 while (x<100) { vector#x# = rnorm(100) x=x+1 } where each vector has, at its hand, instead of #x# a number which goes from 1 to 99. How can I do this? Thanks Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest

Hi all, if I transpose a matrix with t(data), the newly created colums do not appear to have the first row as header. How can I do to have all the newly created columns have their first row as a header? Thanks Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575

Hi, I'm trying to create a frequency histogram for all the values in a table, but when I try to do so, an error is returned, saying that I cannot create a histogram with an obkect of that class. Here's what I do: >library(lattice) >table<-read.table("C:/.../table",header=TRUE,sep="\t") >histogram(table) Please help me!!! Thanks Gabriele Zoppoli, MD

Hello, here is the problem: I want to demonstrate that, on average, the Pearson's correlations of a specified subset of genes from a huge list (>18,000 columns) are higher than any randomly chosen subset of that list. I would therefore like to do a number of tests between that specified subset and randomly chosen ones from the "mother" list. How could I do that? What would be

Hi I'm looking for a package to perform quality control, normalization and analysis of high throughput cell-base chemical screens. I know that the cellHTS2 package provides this for siRNA screens. Does anybody know if something like what I'm looking for exists? Thank you! Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova,

Hi, when I try to import a microarray CEL batch, I get this error message: > myAB <- ReadAffy () Error in .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra, : cannot allocate vector of length 1287151200 which, assuming the value is in bites, is below my RAM values (3 Gb recognized by Windows). The isse is, when I try to do memory.limit (size = 3000 ) the

Sorry, maybe it's easy but I haven't found anything useful: how can I obtain a list C that contains all the members in the list B that are not in list A? This are lists of nanes, not numbers! Thank you Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575

(NPM: new pass manager; LPM: legacy pass manager) In a first quick experiment today I compared code-size of the LMP vs. the NMP for the CSiBE benchmark (and some other), and this shows code-size increases with the NPM that would probably be unacceptable for us. So, now I am wondering how/if we need to mitigate this, and have a bunch of questions. As I've noticed quite some activity around

Please give me just a reference where I can find something useful. In summary, I need to : - find the median of each row of a matrix - create a new matrix with each value in the first matrix divided by the median of its row - if a value "a" in the second matrix is < 1, I need to substitute it with 1/a I know that for some of you it must be overeasy, but I swear I googled for two

Hello! I have this problem: I want to create a Venn's diagram with three lists of genes'names. The first is all the genome, the second a subset of it comprising all mitochondrial genes, and the third including all genes that correlate with a given gene. This is what I do: > library(gplots) > A<-read.delim("F:/.../mito genes just names.txt") >

Hi, I have a dataset with 6 categorical variables. I have used this following code to make the variables u1-u6 ordered factors and this works well. cat1cat2 cat3 cat4 cat5 cat6 ? 0 ? ?? 1 ? ? 1????? 0 ??? 0? ?? 1 ? 1 ? ?? 1 ? ? 0 ? ?? 0 ? ? 0 ? ? 0 ....... .... ############ data<-read,table("example.txt") data <- as.data.frame(lapply(data, ordered)) ############ Now,