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03-06-2019, 11:11 AM
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Member
Location: Italy Join Date: Jul 2017
Posts: 34
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error in DESeqDataSet
Dear all,
I have 4 RNAseq file from an experiment with two different conditions, "Untreated" and "Treated" and after thee counting of the reads with futureCounts I'm trying to analyze it with DESeq2, here the command lines Code:
countdata <- as.matrix(read.table("'/DESeq2_STAR/count.table", header=TRUE, row.names=1))
head (countdata)
condition <- factor(c(rep("Untreated",2), rep("Treated",2)))
coldata <- data.frame(row.names=colnames(countdata),condition)
head(coldata)
library("DESeq2")
dds <- DESeqDataSetFromMatrix(countdata, coldata, design=~condition)
everything is ok until the last command line, Code:
> dds <- DESeqDataSetFromMatrix(countdata, coldata, design=~condition) Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are not integers I don't understand what is not integers? My table look similar to those describe in DESeq2 vignettes Code:
mapping.star.PF382 mapping.star.SUPT1 mapping.star.SUPT13 mapping.star.RPMI8402 ENSG00000223972 7.12 119.48 27.45 58.49 ENSG00000227232 2793.80 2410.36 1630.14 2960.74 ENSG00000243485 30.00 2.93 20.52 16.32 ENSG00000237613 0.00 0.00 1.83 1.00 ENSG00000268020 1.00 0.00 0.50 0.00 ENSG00000240361 0.00 0.00 0.00 0.00 |
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