search for: ngene

...--BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I'm trying to understand some C code in an R package I'm using. I'm address this question here as it's matrix algebra...and I'm no pro at that! the C command reads: double alpha = 1.0, beta = 0.0; dsyrk_("L", "N", nGenes, nGenes, & alpha, mat1, nGenes, & beta, mat2, nGenes); - From google, I've found out that dsyrk is for performing one of the symmetric rank k operations - whatever that means!? From here: http://linux.die.net/man/l/dsyrk I've found that the calculation being performed is...

Dear List, I am trying to modify the xlab and ylab for a current figure that was plotted by a package, I searched through the low level plotting command and they do not seem to contain how to do this (the only way is to use xlab, ylab as arguments in "plot" command, which I can not do since the plot is plotted using some other package, not by my own script). Is there any command for

...#line1 setwd('/root/subroot') # line 2 load('imge.RData') # line3 imge <- imge[,-c(3)] # line4 imge <- imge[complete.cases(imge),] # line5 trait<- read.csv(trait.file) # line6 ngenes <- nrow(imge) # line7 nsnp <- nrow(trait) #line 8 for(i in 1:ngenes) { for(j in 1:nsnp) { if(imge$d1[i]==trait$d1[j] & imge$d2[i]==trait$d2[j]) trait$imgene2[j] <- imge$Gene[i] else trait$imgene2[j] <- NA } } return(trait...

...: chr [1:10788, 1:8] "10836" "22277" "1243" "10509" ... ..- attr(*, "dimnames")=List of 2 .. ..$ : NULL .. ..$ : chr [1:8] "Row" "Gene ID" "Gene Name" "Score(d)" ... $ color.ind.for.multi: NULL $ ngenes.up : int 9769 $ ngenes.lo : int 10788 So I guess I have 9769 up-regulated and 10788 down-regulated genes. The problem is, that not all of them are above 2fold: > head(siggenes.table$genes.up) Row Gene ID Gene Name Score(d) [1,] "6587"...

Hello R-community, It's been a week now that I am struggling with the implementation of a cox model in R. I have 80 cancer patients, so 80 time measurements and 80 relapse or no measurements (respective to censor, 1 if relapsed over the examined period, 0 if not). My microarray data contain around 18000 genes. So I have the expressions of 18000 genes in each of the 80 tumors (matrix

...no disease, 17 disease) this code: set.seed(100) y <-c(rep(0,20),rep(1,17)) genenames<-as.character(data$Gene.Symbol) geneset<-as.character(rownames(x)) GSA.obj<-GSA.func(x,y, genenames, geneset, resp.type="Two class unpaired") returns this error: Error in 1:max(ngenes, na.rm = TRUE) : result would be too long a vector In addition: Warning message: In max(ngenes, na.rm = TRUE) : no non-missing arguments to max; returning -Inf Could someone explain the error? I have performed this analysis with the globaltest package without problems. SessionInfo() R versio...

...which(y==Ytype[1])] <- 1 yy[which(y==Ytype[2])] <- -1 y <- yy ## check ladder if( min(diff(ladder)) >= 0 ) { print("ERROR!! ladder must be monotonously decreasing") return(0); } if( ladder[1] != ncol(x) ) { ladder <- c(ncol(x), ladder) } nSample <- nrow(x) nGene <- ncol(x) SampInd <- seq(1, nSample) if( CVtype == "LOO" ) { CVnum <- nSample } else { if( CVnum == 0 ) { CVnum <- nSample } } ## vector for test error and number of tests ErrVec <- vector( length=length(ladder)) names(ErrVec) <- paste("Lev_", la...

...sam in package siggenes do not have var.equal option ? Are there some reason ? sam(data,cl,B=100,balanced=FALSE,mat.samp=NULL,delta=(1:10)/5,med.fdr=TRUE,s 0=NA,alpha.s0=seq(0,1,.05),include.s0=TRUE,p0=NA,lambda.p0=1,vec.lambda.p0=( 0:95)/100, na.rm=FALSE,graphic.fdr=TRUE,thres.fdr=seq(0.5,2,0.5),ngenes=NA,iteration=3, initial.delta=c(.1,seq(.2,2,.2),4),rand=NA) Any help is greatly appreciated. Sincerely. Liu Yu Ting

...sCore Attaching package: 'affyPLM' The following object(s) are masked from 'package:stats': resid, residuals, weights *** caught segfault *** address 0xc609000, cause 'memory not mapped' Traceback: 1: .Call("rma_c_complete", probeintensities$pm, pNList, ngenes, normalize, background, bgversion, verbose, PACKAGE = "affy") 2: just.rma(filenames = l$filenames, phenoData = l$phenoData, description = l$description, notes = notes, compress = compress, rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, verbose = verbose,...

...hr3 132601066 132601066 A G exonic ACKR4 655 chr3 132601999 132601999 A G exonic BCDF5,CDFG6", header=TRUE,stringsAsFactors=FALSE) multgenes<-grep(",",df.sample.gene$Gene.refGene) rep_genes<-strsplit(df.sample.gene$Gene.refGene[multgenes],",") ngenes<-unlist(lapply(rep_genes,length)) dup_row<-function(x) { newrows<-x lastcol<-dim(x)[2] rep_genes<-unlist(strsplit(x[,lastcol],",")) for(i in 2:length(rep_genes)) newrows<-rbind(newrows,x) newrows$Gene.refGene<-rep_genes return(newrows) } for(multgene in multgen...

I would appreciate please a suggestion on how to do the following : i'm working with a dataframe in R that contains in a specific column multiple gene names, eg : > df.sample.gene[15:20,2:8] Chr Start End Ref Alt Func.refGene Gene.refGene284 chr2 16080996 16080996 C T ncRNA_exonic GACAT3448 chr2 113979920 113979920 C T ncRNA_exonic LINC01191,LOC100499194465

...G exonic ACKR4 > 655 chr3 132601999 132601999 A G exonic BCDF5,CDFG6", > header=TRUE,stringsAsFactors=FALSE) > > multgenes<-grep(",",df.sample.gene$Gene.refGene) > rep_genes<-strsplit(df.sample.gene$Gene.refGene[multgenes],",") > ngenes<-unlist(lapply(rep_genes,length)) > dup_row<-function(x) { > newrows<-x > lastcol<-dim(x)[2] > rep_genes<-unlist(strsplit(x[,lastcol],",")) > for(i in 2:length(rep_genes)) newrows<-rbind(newrows,x) > newrows$Gene.refGene<-rep_genes > return(newro...

...DM1105 Adapters # CONFIG_DVB_DM1105=m # # Supported FireWire (IEEE 1394) Adapters # CONFIG_DVB_FIREDTV=m CONFIG_DVB_FIREDTV_INPUT=y # # Supported Earthsoft PT1 Adapters # CONFIG_DVB_PT1=m # # Supported Mantis Adapters # CONFIG_MANTIS_CORE=m CONFIG_DVB_MANTIS=m CONFIG_DVB_HOPPER=m # # Supported nGene Adapters # CONFIG_DVB_NGENE=m # # Supported ddbridge ('Octopus') Adapters # CONFIG_DVB_DDBRIDGE=m # # Supported DVB Frontends # CONFIG_DVB_FE_CUSTOMISE=y # # Customise DVB Frontends # # # Multistandard (satellite) frontends # CONFIG_DVB_STB0899=m CONFIG_DVB_STB6100=m CONFIG_DVB_STV090x=...

...DM1105 Adapters # CONFIG_DVB_DM1105=m # # Supported FireWire (IEEE 1394) Adapters # CONFIG_DVB_FIREDTV=m CONFIG_DVB_FIREDTV_INPUT=y # # Supported Earthsoft PT1 Adapters # CONFIG_DVB_PT1=m # # Supported Mantis Adapters # CONFIG_MANTIS_CORE=m CONFIG_DVB_MANTIS=m CONFIG_DVB_HOPPER=m # # Supported nGene Adapters # CONFIG_DVB_NGENE=m # # Supported ddbridge ('Octopus') Adapters # CONFIG_DVB_DDBRIDGE=m # # Supported DVB Frontends # CONFIG_DVB_FE_CUSTOMISE=y # # Customise DVB Frontends # # # Multistandard (satellite) frontends # CONFIG_DVB_STB0899=m CONFIG_DVB_STB6100=m CONFIG_DVB_STV090x=...