search for: countdata

...2? 0? 1? 1 #6???????? aAAAAAGAGPEMVR 1-n_acPro/ 2? 0? 0? 2 resCounts<- f(lista,FacGroup) t.test.p.value <- function(...) { ??? obj<-try(t.test(...), silent=TRUE) ??? if (is(obj, "try-error")) return(NA) else return(obj$p.value) ?} #3rd function for p-value fpv<- function(Countdata){ resNew<-do.call(cbind,lapply(split(names(Countdata)[4:ncol(Countdata)],gsub("[0-9]","",names(Countdata)[4:ncol(Countdata)])), function(i) {x<-if(ncol(Countdata[i])>1) rowSums(Countdata[i]) else Countdata[i]; colnames(x)<-NULL;x})) indx<-combn(names(resNew),2) r...

...mited .txt) appears to be correct: >head(myfile) VZ_w13 VZ_w14a VZ_w14b VZ_w15a VZ_w15b VZ_w16a ENSG00000253101 0 0 0 0 0 0 ENSG00000223972 0 0 0 0 0 0... However, when I try to analyze the data with >cds <- newCountDataSet(myfile,conds) I get the following message: "Error in newCountDataSet(myfile,conds) : The countData is not integer. The problem, as far as I can tell, is that my data are numerical, not integer, because when I run >str(myfile) 'data.frame': 53433 obs. of 14 variables: $ VZ...

...ta and design formula. library("DESeq2") countMatrix = read.table("read_count.22May.2017.new.txt",header=T,sep='\t',check.names=F) head(countMatrix) dim(countMatrix) [1] 57894 35 Now I am not sure how to construct a DESeqDataSet: dds <- DESeqDataSetFromMatrix(countData = countMatrix, colData = colData, design = ~ condition) Thanks Yogesh -- *Yogesh Gupta* *Postdoctoral Researcher* *Department of Biological Science* *Seoul National University* *Seoul, South Korea* [[alternative HTML version deleted]]

...oon: the moon phase (new or full). position: a random factor (I had 4 foraging stations) individual_id: a random factor indicating the individual foraged in the tray. This is the lmer parameters I have used: model<-lmer(count~ta*habitat*season*moon + (1|individual_id) + (1|position), data=countdata, family=poisson) I would really appreciate the help. I love working with R and it really changed the way I work with my data. Thanks again, Ofir. -- View this message in context: http://www.nabble.com/doing-zero-inflated-glmm-for-count-data-with-fmr-tp23136570p23136570.html Sent from the R help...