``` r
dds_energetic_state_GO <- DESeqDataSetFromMatrix(countData = energetic_state_GO_genes_filt, 
                              colData = metadata, 
                              design = ~Timepoint+ColonyID)
```

```
## converting counts to integer mode
```

```
## 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
# Variance Stabilizing Transformation
vsd_energetic_state_GO <- varianceStabilizingTransformation(dds_energetic_state_GO, blind = TRUE)  # Must use varianceStabilizingTransformation() instead of vst() due to few input genes
```

```
##   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
vsd_energetic_state_GO <- assay(vsd_energetic_state_GO)
```