When I use DESeq, I don't seem to be able to get the newCountDataSet to work. I get this error:
> cds <- newCountDataSet(mydata,conds)
Error in round(countData) : Non-numeric argument to mathematical function
> head(mydata)
V1 V2 V3
1 zhu1_Ghi#S28631427 8.9990205 10.5918948
2 zhu1_Ghi#S28631527 0.4181748 0.3937552
3 zhu1_Ghi#S28631546 7.4275293 24.3262365
4 zhu1_Ghi#S28631624 11.5885114 9.8558116
5 zhu1_Ghi#S28631691 0.8391944 10.7992493
6 zhu1_Ghi#S28631709 3.8783566 4.2137042
> str(mydata)
'data.frame': 18634 obs. of 3 variables:
$ V1: Factor w/ 18634 levels "zhu1_Ghi#S28631416",..: 2 4 5 6 7 8 9 10 11 12 ...
$ V2: num 8.999 0.418 7.428 11.589 0.839 ...
$ V3: num 10.592 0.394 24.326 9.856 10.799 ...
How can I solve this problem?
> cds <- newCountDataSet(mydata,conds)
Error in round(countData) : Non-numeric argument to mathematical function
> head(mydata)
V1 V2 V3
1 zhu1_Ghi#S28631427 8.9990205 10.5918948
2 zhu1_Ghi#S28631527 0.4181748 0.3937552
3 zhu1_Ghi#S28631546 7.4275293 24.3262365
4 zhu1_Ghi#S28631624 11.5885114 9.8558116
5 zhu1_Ghi#S28631691 0.8391944 10.7992493
6 zhu1_Ghi#S28631709 3.8783566 4.2137042
> str(mydata)
'data.frame': 18634 obs. of 3 variables:
$ V1: Factor w/ 18634 levels "zhu1_Ghi#S28631416",..: 2 4 5 6 7 8 9 10 11 12 ...
$ V2: num 8.999 0.418 7.428 11.589 0.839 ...
$ V3: num 10.592 0.394 24.326 9.856 10.799 ...
How can I solve this problem?
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