Question: rlog() is not working ?
0
gravatar for shn_yns
4 weeks ago by
shn_yns0
shn_yns0 wrote:

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.

deseq2 • 87 views
ADD COMMENTlink modified 4 weeks ago by Michael Love25k • written 4 weeks ago by shn_yns0
Answer: rlog() is not working ?
0
gravatar for Michael Love
4 weeks ago by
Michael Love25k
United States
Michael Love25k wrote:

Can you use vst() instead? I haven’t seen this error but it probably means the rlog() model isn’t a good fit. Anyway I prefer vst() for transformation.

ADD COMMENTlink written 4 weeks ago by Michael Love25k

Thank you very much for reply. I have tried vst() instead of rlog(). It worked well.

ADD REPLYlink written 4 weeks ago by shn_yns0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 182 users visited in the last hour