Hi All,
I am doing rRNA reduced, strand specific RNA-seq in bacterial species and decided to try EDGE-pro (Estimated Degree of Gene Expression in Prokaryotic Genomes) and then run the count table in DESeq.
I have four treatments and three replicates each. When I try to compare the three replicates of the untreated wild-type strain with three replicates of the treated wild-type strain DESeq runs for >10 hours and has thrown an error about running out of memory.
Using Bioconductor version 2.12 (BiocInstaller 1.10.1), R version 3.0.0.
countTable <- read.table("deseqFile_WT.txt", header=T, sep="\t", row.names=1)
expt_design <- data.frame(row.names = colnames(count_table),condition = c("WT_UT","WT_UT","WT_UT","WT_T","WT_T","WT_T"))
conditions = expt_design$condition
library("DESeq")
cds <- newCountDataSet(countTable, conditions)
cds <- estimateSizeFactors(cds)
cds <- estimateDispersions(cds)
results <- nbinomTest(cds, "WT_UT", "WT_T")
= no output, 100% CPU and >10-12 hours later...
Any help is greatly appreciated.
I am doing rRNA reduced, strand specific RNA-seq in bacterial species and decided to try EDGE-pro (Estimated Degree of Gene Expression in Prokaryotic Genomes) and then run the count table in DESeq.
I have four treatments and three replicates each. When I try to compare the three replicates of the untreated wild-type strain with three replicates of the treated wild-type strain DESeq runs for >10 hours and has thrown an error about running out of memory.
Using Bioconductor version 2.12 (BiocInstaller 1.10.1), R version 3.0.0.
countTable <- read.table("deseqFile_WT.txt", header=T, sep="\t", row.names=1)
expt_design <- data.frame(row.names = colnames(count_table),condition = c("WT_UT","WT_UT","WT_UT","WT_T","WT_T","WT_T"))
conditions = expt_design$condition
library("DESeq")
cds <- newCountDataSet(countTable, conditions)
cds <- estimateSizeFactors(cds)
cds <- estimateDispersions(cds)
results <- nbinomTest(cds, "WT_UT", "WT_T")
= no output, 100% CPU and >10-12 hours later...
Any help is greatly appreciated.
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