Hi all I am using HT-Seq count data to analyze differential expression with DESeq2 in R. I have about 60000 genes(all coding+non-coding genes) and 159 patients (two group, 0=66, 1=93). *Is this ok to use both coding and non-coding genes? or I should remove non-coding genes first? *Also, with DESeq2 I get this warning message. Is this effective on result or this is fine to have this warning? And how can I solve this?
rdata <- read.table("data.txt", header = TRUE, row.names = 1) library(DESeq2) ## Create metadata sample_org <- data.frame(row.names = colnames(rdata), c(rep("0", 66), rep("1", 93))) colnames(sample_org) <- c("Group") dds <- DESeqDataSetFromMatrix(countData = rdata, colData = sample_org, design = ~Group) dd <- DESeq(dds) res <- results(dd) #Saving results write.csv(res,"res.csv")
in this part I get warning:
dds <- DESeqDataSetFromMatrix(countData = rdata, colData = sample_org, design = ~Group)
The warning message is:
Warning message: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors