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Old 03-06-2019, 10:11 AM   #1
NDUFB11
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Location: Italy

Join Date: Jul 2017
Posts: 27
Default 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
Thank you
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