similar to: Selecting the "non-attribute" part of an object

I want to get the count matrix of genes from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146049. Is it possible for GSE146049? After getting counts, I want to do TMM normalization. [[alternative HTML version deleted]]

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

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 at 11:09?PM Anas Jamshed <anasjamshed1994 at gmail.com> wrote: > > I want to get the count matrix of genes from >

I am running R 2.2.1 on a University-supported linux installation based on Redhat EL3. I am sorry that it did not occur to me to mention this before; I updated R very recently, with the most recent version available for EL3 at http://cran.cnr.berkeley.edu/bin/linux/redhat/el3/. Looking at the gridBase documentation, I find that 2.2.1 is not in fact the most recent version. I have now spent

Under Details, the documentation says "[if Rowv or Colv] is 'NULL', _no reordering_ will be done for the corresponding side." In fact, as explained elsewhere in the documentation, 'NA' is required, not 'NULL'. An anonymous expert suggested that I should attach an svn diff file to this report, so I will. JD -------------- next part -------------- Index:

On 2002.10.19 19:44 Ruben I Safir wrote: NYLXS is having a watershed week this week and I'd like to personally extend my hope to everyone to participate and prosper from all of our activities. On Sunday, We are papering Long Island City and Astoria with Flyers for the Free Software Business Demo at LaGaurdia College. We are meeting at the front Entrance of the Queens Citicorp Building

The hybrid feature in fisher.test looks to me like an excellent way to analyze my two-way tables. The only problem is that it does not seem to be implemented. Am I right about this? An example is pasted below. I note that I get the warning message only when I shouldn't: for a 2x2 table hybrid seems to be ignored without warning. In no case does fisher.test seem to be checking Cochran

Is there a way to use ssh tunnels to access samba shares on a remote system from a Win 2K box? I have some linux boxen behind a NAT in a data center, and someone wants samba access to to one of them. No way in hell am I opening it through the NAT. Thanks. -- Justin Georgeson UnBound Technologies, Inc. http://www.unboundtech.com Main 713.329.9330 Fax 713.460.4051 Mobile 512.789.1962 5295

As instructed, I have spent a long time searching the web for an answer to this question. I am trying to use Sweave to produce lecture slides, and have the problem that I can't control the formatting of my R source. Setting options(width), as recommended in this forum, works fine on the R _output_, but seems to have unpredictable effects on the echoing of the source code. If I try setting

Dear all, Let's say I have the following: # Loading the boot package # install.packages(boot) library(boot) # Generating data set.seed(123) x <- rnorm(100) # Bootstrap for the sample mean bmean <- boot(x, function(x,d) mean(x[d]), R=1000) bmean # #ORDINARY NONPARAMETRIC BOOTSTRAP # # #Call: #boot(data = x, statistic = function(x, d) mean(x[d]), R = 1000) # # #Bootstrap Statistics : #

All, I am attempting to select all of the contiguous elements of a matrix that meet some criterion. I.e., values that would be contained within an irregular area defined by a "contour" applied around point of interest. So, if I have a matrix x as follows: > x <- matrix(rnorm(25), nrow=5, ncol=5,

Hello, I'm hoping someone with a wide experience with R may be able to see what the program is trying to tell me. I've got an array: y1=rnorm(41,0.2) y2=rnorm(41,0.2) y3=rbind(y1,y2) data11<-array(0,c(41,2,2)) data11[,1,]=y3 data11[,2,]=y3 rownames(data11)<-rownames(data11, do.NULL = FALSE, prefix = "Obs.") colnames=c("V","R")

I have a list of observations of individuals. I would like to make a list of individuals, with a data frame of observations for each individual. The following code usually works, but not always ---------------------------------------------------------------------- # Make a list of empty data frames animals = list() indivs = levels(Z$individual_id) donotprint <- sapply(indivs, function(i){

Dear list, If anyone knows how to assign dimnames to matrices or arrays I would be most grateful for help. I've tried various permutations of likely-looking code but get error messages every time. I could find no example in the documentation. Many thanks, Dan Bebber Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 3RB UK Tel. 01865 275000

Hi, I was bitten by a little incoherence in dimnames assignment or may be I missed some point. Here is the case. If I assign row names via dimnames(a)[[1]], when nrow(a)=1 then an error is thrown. But if I do the same when nrow(a) > 1 it's OK. Is one of this case works unexpectedly? Both? Neither? a=as.matrix(1) dimnames(a)[[1]]="a" # error: 'dimnames' must be a list

I have a matrix y: > dimnames(y) $x93 [1] "1" "2" $x94 [1] "0" "1" "2" .................. so on (there are other dimensions as well) I need to access a particular dimension, but a random mechanism tells me which dimension it would. So, sometimes I might need to access dimnames(y)$x93, some other time it would be dimnames(y)$x94.. and so

Hello, the fix of PR18612 (https://bugs.r-project.org/show_bug.cgi?id=18612) in r85380 (https://github.com/wch/r-source/commit/2653cc6203fce4c48874111c75bbccac3ac4e803) caused a change in `dim<-()`. Specifically, in the past, any `dim<-()` assignment would _always_ remove "dimnames" and "names" attributes per help("dim"): The replacement method changes

>>>>> Henrik Bengtsson >>>>> on Sun, 29 Oct 2023 10:42:19 -0700 writes: > Hello, > the fix of PR18612 > (https://bugs.r-project.org/show_bug.cgi?id=18612) in > r85380 > (https://github.com/wch/r-source/commit/2653cc6203fce4c48874111c75bbccac3ac4e803) > caused a change in `dim<-()`. Specifically, in the past,

Hi Martin, Henrik, I actually like this change. Makes a lot of sense IMO that dim(x) <- dim(x) be a no-op, or, more generally, that foo(x) <- foo(x) be a no-op for any setter/getter combo. FWIW S4Arrays::set_dim() does that too. It also preserves the dimnames if the right value is only adding or dropping outermost (ineffective) dimensions: ??? > x <- array(1:6, dim=c(2,3,1),

Dear all, is there anyone who can help me extracting p-values from an Anova object from the car library? I can't seem to locate the p-values using str(result) or str(summary(result)) in the example below > A <- factor( rep(1:2,each=3) ) > B <- factor( rep(1:3,times=2) ) > idata <- data.frame(A,B) > fit <- lm( cbind(a1_b1,a1_b2,a1_b3,a2_b1,a2_b2,a2_b3) ? sex,