deseq2 datasetfrommatrix
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Chay • 0
@235c1561
Last seen 2.3 years ago
United Kingdom
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))

i get this error

Error in DESeqDataSet(se, design = design, ignoreRank) : 
  some values in assay are negative
DESeq2 • 832 views
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@james-w-macdonald-5106
Last seen 9 hours ago
United States

Yes. You are meant to be providing counts and some are negative. Since you can't count things and get negative numbers, there is a problem with the counts you are supplying. You should figure out why.

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