deseq2 datasetfrommatrix
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Chay • 0
@235c1561
Last seen 4 weeks 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 • 242 views
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@james-w-macdonald-5106
Last seen 18 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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