I want to have sample names from my summarized experiment (se) in my created DESeqDataSet (dds). I would like to look at the counts data in assay(dds) with sample names rather than the numeric headers that exist:

assay(dds)

results in:

[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]

ENSG00000000003 0 0 0 2 0 0 0 0

ENSG00000000005 0 0 0 0 0 0 0 0

ENSG00000000419 712 479 689 597 922 906 647 930

How would you associate [,1] [,2]... etc with 1_sample that you can see in:

colData(se) <- DataFrame(sampleTable)

DataFrame with 8 rows and 4 columns

          sample_id Type    Time     Cell

          <factor>  <factor> <factor> <factor>
  

1 1_sample n 0 4

2 2_sample n 0 8

3 3_sample y 0 4

4 4_sample y 0 8

5 5_sample n 24 4

6 6_sample n 24 8

7 7_sample y 24 4

8 8_sample y 24 8

to create:

1sample 2sample 3sample 4sample 5sample 6sample 7sample 8sample

ENSG00000000003 0 0 0 2 0 0 0 0

ENSG00000000005 0 0 0 0 0 0 0 0

ENSG00000000419 712 479 689 597 922 906 647 930

I think all you need to do is give your sampleTable rownames.