``` r
dds_Apul_lncRNA <- DESeqDataSetFromMatrix(countData = Apul_counts_lncRNA,
                              colData = coldata,
                              design = ~ time.point + colony.id)
```

```
## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors
```

```
##   Note: levels of factors in the design contain characters other than
##   letters, numbers, '_' and '.'. It is recommended (but not required) to use
##   only letters, numbers, and delimiters '_' or '.', as these are safe characters
##   for column names in R. [This is a message, not a warning or an error]
```

``` r
dds_Apul_lncRNA
```

```
## class: DESeqDataSet 
## dim: 20559 40 
## metadata(1): version
## assays(1): counts
## rownames(20559): lncRNA_001 lncRNA_002 ... lncRNA_24182 lncRNA_24183
## rowData names(0):
## colnames(40): 1A1_ACR-173_TP1 1A10_ACR-145_TP4 ... 2F1_ACR-265_TP1
##   2G1_ACR-145_TP2
## colData names(2): time.point colony.id
```