Differential expression analysis with DESeq2

Question

[Rob]

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

Answer 1

[swbarnes2]

Don't worry about the warning. Unless you want to use the metadata numerically, you want them to be factors.

Answer 2

[Spencer]

just ignoring it. in most cases we need to set stringsAsFactors False to prevent unexpected error