similar to: random sample from arrays

hi I want to compare two list by its names and get the values of that list. can anybody let me know the syntax of comparing the list by their names using a for loop c.genes<- list() for(i in 1:100) c.genes[[1]]<- geneset(which(geneset == tobecampared[i])) } here geneset is a list and also tobecampared is a list Thank you Ramya -- View this message in context:

Hallo, > fit12<-lmFit(qrg[,1:2]) > t12<-toptable(fit12,adjust="fdr",number=25,genelist=qrg$genes[,1]) > t12 ID logFC t P.Value adj.P.Val B 522 PLAU_OP -6.836144 -8.420414 5.589416e-05 0.01212520 2.054965 1555 CD44_WIZ -6.569622 -8.227938 6.510169e-05 0.01212520 1.944046 Can anyone tell me what the difference is between P.Value

Dear All: I tried to use heatmap.2 to generate hierarchical clustering using the following command: heatmap.2(datamatrix, scale="row", trace="none", col=greenred(256), labRow=genelist[,1], margins=c(10,10), Rowv=TRUE, Colv=TRUE) datamatrix is subset of a RMA normalized data subset by a genelist. The problem is a lot of times, the z-score in key are from, like -5 to 15 or

Dear sir/madam, I have been using R for a while now for microarray analysis, and I would like to make a "master" data frame in which I can combine information from many different sources. The basic list a genelist with 25.000 probes, then I would like to have a subcompartment with the statistical information, a subcompartment with more extensive information regarding each gene, and then

I am having trouble converting the output from Sweave into a valid PDF file. I have created a simple .Rnw file which will become a full vignette at some point, but during the intermediate testing, I got errors from texi2dvi. This is what I have done. 0) Using a Windows Xp system 1) Created a file called GeneSpring.Rnw 2) Convert this to Tex using Sweave("GeneSpring.Rnw") from within R

Dear R users, I'am using marray and Limma packages to analyze genepix output. 1) how can I filter bad spots from my data (data contains 3 types of bad spots). my experiment contains 12 samples and the bad spot are not associated to the same probes 2) how can I remove control probes from my data ? I'm sorry, i'm new with R and I can't find answer in packages doc. best regards,

Hi, I am using 'igraph' to make some plots. The problem I got is that I don't know how to label the nodes with gene names. My sample code: ## suppose I have 100 gene (nodes) ## --------------------------------------------------------------------------- graph <- set.vertex.attribute(graph, "color", value=c(rep(c('green','red'),50))) graph <-

Hallo, how can I store a variable as a tab-delimited txt-file? I crated a variable with the following commands: > fit12<-lmFit(qrg[,1:2]) > t12<-toptable(fit12,adjust="fdr",number=25,genelist=qrg$genes[,1]) > t12 ID logFC t P.Value adj.P.Val B 522 PLAU_OP -6.836144 -8.420414 5.589416e-05 0.01212520 2.054965 1555 CD44_WIZ -6.569622

Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the genomic coordinates. Furthermore I have no clue how to deal with the fact, that most genes have