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shn_yns
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@shn_yns-21933
Last seen 4.5 years ago
I have a dataset which contain 18 variables in 6 different condition with three replicates. the codes as below.
readcounts <- read.table("../u_counts.txt", header = TRUE)
row.names(readcounts) <- readcounts$Geneid
readcounts <- readcounts[,-c(1:6)]
names(readcounts) <- c("100_1","100_2","100_3",
"200_1","200_2","200_3",
"300_1","300_2","300_3",
"400_1","400_2","400_3",
"500_1","500_2","500_3",
"600_1","600_2","600_3")
growscale <- c(rep(c("100","200","300","400","500","600"), each=3))
sample_info <- data.frame(condition=growscale, row.names=names(readcounts))
DESeq.ds <- DESeqDataSetFromMatrix (countData = readcounts,
colData = sample_info,
design = ~ condition )
DESeq.ds <- DESeq.ds[rowSums(counts(DESeq.ds)) > 0,] #eleminate counts that are less than zero
DESeq.ds <- estimateSizeFactors(DESeq.ds)
sizeFactors(DESeq.ds)
DESeq.rlog <- rlog(counts(DESeq.ds), blind = TRUE)
and i am getting a error as below;
Error in approx(cumsum(wts), x, xout = c(low, high), method = "constant", :
zero non-NA points
In addition: Warning message:
In xy.coords(x, y, setLab = FALSE) : NAs introduced by coercion
Could anyone please help? Thanks in advance.
Thank you very much for reply. I have tried vst() instead of rlog(). It worked well.