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Hi, R-help, I have a group of data from RNA-seq want to be analyzed by Fisher's exact test in R. I want to compare the significant difference of about 30,0000 individuals in two different samples, and I have no idea how to use R, so could you please give me some suggestions or the scripts for Fisher's exact test? Thank you very much. Best, Guanfeng Wang [[alternative HTML version

Is anyone aware of a fast way of doing fisher's exact test for a series of 2 x 2 tables in R? The fisher.test is really slow if n1=1000 and n2 = 1000. -- Thanks, Jim. [[alternative HTML version deleted]]

I have a very basic question about limma. Assume I have experiments from 3 or more RNA sources in a reference design. It is easy to define individual contrasts but I want to specify a contrast matrix that tests for significant differences among ALL the different RNA sources (i.e. the analogous thing to a simple One-Way ANOVA). How can I do that? Thanks! Max --

Hello everyone, Can someone tell me exactly how to generate data from a null distribution for the fisher exact test? I know I have to use the hypergrometric but exactly what commands do I use? Jim [[alternative HTML version deleted]]

Full_Name: Thomas Richardson Version: R 2.9.0 GUI 1.28 Tiger build 32-bit (5395) OS: 10.4.11 Submission from: (NULL) (216.254.15.72) I have encountered a problem with points in scatterplots disappearing in a quartz window when it is re-sized (to make it larger). I am constructing an 8x12 matrix of scatterplots each containing approx 600 points. In order to get them in the window I remove the

Hi All I am wondering if people based on their experience could share what methods one could use to compare two gff/gtf files. The reason why I want to do so is that we have constructed a RNA-Seq based transcriptome and would like to compare it with reference transcriptome we had from in-silico approaches. Ideally we are looking to find out 1. new genes we see 2. transcripts where the

Dear all, I have a question about limmaGUI that is usually run in R environment. My problem is loading data into the programm. I have 6 gpr files that apparently are not compatible with limma. Everytime I'm trying to load the data (including a RNA targets file, an error appears:Error reading files. that I'm not sure,but seems to have something to do with the format of my files

Hi, I have a microarray dataset from Agilent chips. The data were really log ratio between test samples and a universal reference RNA. Because of the nature of log ratios, coefficient of variation (CV) doesn't really apply to this kind of data due to the fact that mean of log ratio is very close to 0. What kind of measurements would people use to measure the dispersion so that I can compare

I have a matrix with 2 columns and I want to do fishers exact test for these with the totals for each row being 100 say. The data has the form: 23 12 32 21 12 2 and these represents the tables: 23 12 77 88 32 21 78 79 12 2 88 98 How do I use apply to speed up aclculation of the fisher.exact test? -- Thanks, Jim. [[alternative HTML version deleted]]

Hi, I'm using GAGE/pathview to analyze my RNA-seq and phospho-protein data. The following error occurs after this command line below: >pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview( gene.data = cnts.d, pathway.id = pid, gene.idtype="SYMBOL",kegg.native = F, same.layer = T, species = "hsa", kegg.dir = "test", out.suffix = "up"))

Hello, all, I'm a new R user (new to any programming language in general, really), so I apologize if this is easy/has already been answered (I've attempted searching online but did not understand the pages I found). My data is stored in text files with the headers LANE, RNA_NAME, SEQ, and SEQCNT. I've been using x = "filename.txt" y = aggregate(x$SEQCNT, list(x$RNA_NAME),

Fisher is not the only person that it may be necessary to read 4 or 5 times. The same may be the case for side comments that Bill Venables is wont to make. Now to the parallel universe that I have in mind. I wonder whether the time is opportune for a list that focuses on "Statistical Methodology for R Users". The difference from other statistical methodology lists is that it will be

It might have a noticeable effect on clients. I encountered (probably triggered by this in some way?) that I was unable to het the 'read' bit set in macOS Mail.app. Maybe (as I am doing HA with round robin) the Mail.app client got to one dovecot repository on one tcp connection and then on the other. Is there a reason why syncing tis move from new to cur is a bad idea? Gerben Wierda

Hello, I am a total beginner with ?R? and found a package ?venn? to create a venn diagram. The problem is, I cannot create the vectors required for the diagram. The manual say: "R> venn(accession, libname, main = "All samples") where accession was a vector containing the codes identifying the RNA sequences, and libname was a vector containing the codes identifying the

Hi everyone, I'm trying to generate an RNA degradation plot of the Estrogen example data plot, but seem to get an error. I've tried defining an ylim value, ylim=c(0,30) , but it doesn't seem to work either. My code is as follows: > RNAdeg<-AffyRNAdeg(Data) > png(DegLoc, width=720, height=720) > par(ann=FALSE) > par(mar=c(3,3,0.1,0.1)) >

How can I subscribe to R genomic list? On Sun, 2 Apr 2023, 9:28 pm Peter Langfelder, <peter.langfelder at gmail.com> wrote: > It's a microarray data set, so I don't think you would want to apply > an RNA-seq pipeline. You'd be better off applying a normalization > appropriate for this type of microarray data. > > HTH, > > Peter > > On Sun, Apr 2, 2023

I have a matrix say, 1 4 23 30 and I want to find the previously attainable fisher's exact test p-value. Is there a way to do this in R? -- Thanks, Jim. [[alternative HTML version deleted]]

On January 6, 2023 3:56:39 AM GMT+02:00, Gerben Wierda <gerben.wierda at rna.nl> wrote: >One step further in my quest to create a replacement mail server. > >I now have my old mail server (2.3.19.1, macOS + MacPorts) and my new (2.3.20, Alpine Linux, Docker, apk package). When I turn on replication it works, but, after a while I see: > >Jan 06 00:50:31 replicator: Panic: data

Hi, I am trying to using SAMseq() to analyze my RNA-seq experiment (20000 genes x 550 samples) with survival endpoint. It quickly give the following error: > library(samr)Loading required package: imputeLoading required package: matrixStats Attaching package: ?matrixStats? The following objects are masked from ?package:Biobase?: ? ? anyMissing, rowMedians Warning messages:1: package ?samr? was

I am considering testing: Ho: Odds Ratio =1 H1: Odds Ratio <>1 How can I generate data from the null distribution for a specific configuration of a Fisher exact test? Jim [[alternative HTML version deleted]]