I am a new user of DESeq2, and encounter problem in creating the DESeqDataSet object. I have counts data from kallisto (kallisto.gene.counts.matrix) with 48 samples that I want to use as an input. And I have created a metadata in .txt format to be combined with the count matrix. The commands I used to upload the files to Rstudio are as follows:
cts = read.table("kallisto.gene.counts.matrix", header=T, row.names=1, com='', check.names=F) cts1 = as.matrix(cts) cts2 = round(cts1)
col_data = read.table(file = "ColData.txt", stringsAsFactors = TRUE, row.names=1, header = T, sep = "\t")
head(coldata) time dmg treat rep NST24rep1 24h no st 1 NST24rep2 24h no st 2 NST24rep3 24h no st 3 NST24rep4 24h no st 4 LST24rep1 24h low st 1 LST24_rep2 24h low st 2
dds <- DESeqDataSetFromMatrix(countData = cts2, colData = col_data, design = ~ soil)
After running the dds script, dds and first_time objects are created in the environment, but it is empty (0 B size or object with null pointer).
View(dds) Warning messages: 1: In class(object) <- "environment" : Setting class(x) to "environment" sets attribute to NULL; result will no longer be an S4 object 2: In class(object) <- "environment" : Setting class(x) to "environment" sets attribute to NULL; result will no longer be an S4 object
Could you please suggest what I could do to make it work and where the mistakes are? Many thanks in advance!