Deseq2 dataframematrix error
Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
I have raw counts of rna seq data with approxx 68 samples, im getting error in deseq dataset can you guys help me
countsTable <-read.csv("counts.csv", header = T, stringsAsFactors = FALSE)
head(countsTable)
sample_info <-read.table("sample.txt", header = T, stringsAsFactors = FALSE)
#rownames(countsTable) <-countsTable[,27902]
#countsTable <-countsTable[,1]
class(sample_info)
sample_info$Type <- as.factor(as.character(sample_info$Type))
library(DESeq2)
rownames(countsTable) <-countsTable[,1]
countsTable <-countsTable[,-1]
(dds<-DESeqDataSetFromMatrix(countsTable[,c(1:128)],colData = sample_info,design = ~Type))
when i run dds<-Deseqdatasetfrommatrix i get this error
{{{Error in DESeqDataSet(se, design = design, ignoreRank) :
some values in assay are negative}}}
My str(countsTable) shows i have int values 0,1,2,3,4 for diff samples
how to run dds for this kindly help.
1 answer
Log in to answer this question.
More posts like this
-
DEG analysis of RNAseq TCGA data AFTER batch effect removal !!!
written by mohammad •
-
Differentially gene expression analysis
written by Nai •
-
Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
written by fernandacarneiro.sc •
-
DESeq2 after GSVA "some values in assay are negative"
written by dew •
-
DESeq2
written by Rob •
-
TCGA single dataset normalization
written by ruby4bioinfo •
-
desEQ2 eRROR
written by Nai •
-
Error using feature counts with DESeq2 : Cannot create DESeqData object
written by VBer
-
[DeSeq2] some values in assay are negative
written by pentium3-user •
-
Error In Deseq2 Analysis
written by 511866357 •
What does
any(countsTable < 0)give you?it gives me FALSE
Some details then please. How did you obtain the counts, and please provide a
head(countsTable).You could also try feeding in truncated versions of the count data until you identify the offending row.