search for: countmatrix

Displaying 3 results from an estimated 3 matches for "countmatrix".

2017 Jun 08
1
DESeq2 pairwise compasion
...o, Pa each with 2 biological replicate. With two biological replicate. I want to do differential gene expression analysis using DESeq2 so I tried these codes after reading about DESeq2: ,my aim is to do the pairwise comparison. how to make colData 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 = ~ conditi...
2017 Jun 21
1
getting error while trying to make dendogram based on gene expression
I am trying to make dendogram based on gene expression matrix , but getting some error: I countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F) colnames(countMatrix) count_matrix <- countMatrix[,-1] # remove first column (gene names) rownames(count_matrix) <- countMatrix[,1] #added first column gene names as rownames) > nonzer...
2017 Jun 22
0
Getting error in dendogram based on gene expression
Dear All, I am trying to make dendogram based on gene expression matrix , but getting some error: I countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F) colnames(countMatrix) count_matrix <- countMatrix[,-1] # remove first column (gene names) rownames(count_matrix) <- countMatrix[,1] #added first column gene names as rownames) > nonzer...