Hi,
I am new to R and trying to carry out hierarchical clustering on an RNA-seq data set (30 different gene.result files).
I am inputting this code:
samples<-read.table("RNAseq_sample3.txt",sep="\t",header=T, fill=TRUE)
files <- list.files("./",pattern=".genes.results")
names(files) <-samples$sample
txi.rsem <- tximport(files, type = "rsem", txIn = FALSE, txOut = FALSE)
txi.rsem$length[txi.rsem$length == 0] <- 1
ddsTxi <- DESeqDataSetFromTximport(txi.rsem, colData = samples,design = ~ Condition)
ddsLRT <- DESeq(ddsTxi, test="LRT", reduced= ~ 1)
resLRT <- results(ddsLRT)
resOrdered <- resLRT[order(resLRT$padj),]
topgenes <- head(rownames(resOrdered),100)
mat <- assay(vsd)[topgenes,]
mat <- mat - rowMeans(mat)
pheatmap(mat,color = colorRampPalette(c("darkblue", "white", "darkred"))(100),border_color = NA,cluster_cols = T,fontsize_row=5,fontsize_col=6)
head(as.data.frame(resOrdered),100)
And this is being returned:
setwd("C:/Users/lmck0/Desktop/RNAseq_gene_results")
samples<-read.table("RNAseq_sample3.txt",sep="\t",header=T, fill=TRUE)
files <- list.files("./",pattern=".genes.results")
names(files) <-samples$sample
txi.rsem <- tximport(files, type = "rsem", txIn = FALSE, txOut = FALSE)
reading in files with read_tsv
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
txi.rsem$length[txi.rsem$length == 0] <- 1
ddsTxi <- DESeqDataSetFromTximport(txi.rsem,colData = samples,design = ~ Condition)
Error in DESeqDataSetFromMatrix(countData = counts, colData = colData, :
ncol(countData) == nrow(colData) is not TRUE
I have googled around why I might be getting this error with the DESeq package but can't seem to work out why...
Any help would be much appreciated!