Hi,

Is this the pipeline you are referring to? https://doi.org/10.1016/j.cels.2019.03.004

If so, it looks like it does provide read counts, but also some RPM (reads per million) files as shown in Table 1. Do you counts contain decimals? If not, it could be that `DESeq2`

is expecting an integer counts matrix and `exceRpt`

is providing an `numeric`

counts matrix.

Here's a small example of how two matrices (`mat`

and `mat2`

) look identical to us, but one of them has `numeric`

and the other one has `integer`

values.

```
## Numeric matrix
mat <- matrix(as.numeric(1:9), ncol = 3)
## Integer matrix
mat2 <- matrix(as.integer(1:9), ncol = 3)
## They look identical
mat
#> [,1] [,2] [,3]
#> [1,] 1 4 7
#> [2,] 2 5 8
#> [3,] 3 6 9
mat2
#> [,1] [,2] [,3]
#> [1,] 1 4 7
#> [2,] 2 5 8
#> [3,] 3 6 9
## But their values are not the same
class(mat[, 1])
#> [1] "numeric"
class(mat2[, 2])
#> [1] "integer"
## We can convert the numeric matrix into an integer one
mat3 <- matrix(as.integer(mat), ncol = 3)
identical(mat2, mat3)
#> [1] TRUE
```

Best,
Leo

PS This was an example for my team on learning how to help others.

Hi Leo,

Thanks for your answer!

That link is the pipeline that I am referring to and my counts do have decimals which is the problem.

Ok. I recommend then 2 things. First, try contacting the authors of

`exceRpt`

directly so they can clarify why the read counts file has decimals.Assuming that it's not a major reason (major reason example: it's not counts, but RPKM values), then you could use something like

`round(mat, digits = 0)`

.Okay awesome thanks for your help!