Hi, I am new to R and trying to carry out unsupervised 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, countData = 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:

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!