DESeq2 problem with resultsNames

Question

[baffiak1902]

Hi, can somebody explain me, where I make mistakes?

I have DESeq sample table:

 SampleName                 countf condition replicate
1       15_3A 15_3A_union_name.count         A         3
2       15_3B 15_3B_union_name.count         B         3
3       15_3C 15_3C_union_name.count         C         3
4       15_3D 15_3D_union_name.count         D         3
5       15_3E 15_3E_union_name.count         E         3
6       20_7A 20_7A_union_name.count         A         7
7       20_7B 20_7B_union_name.count         B         7
8       20_7C 20_7C_union_name.count         C         7
9       20_7D 20_7D_union_name.count         D         7
10      20_7E 20_7E_union_name.count         E         7
11      20_8A 20_8A_union_name.count         A         8
12      20_8B 20_8B_union_name.count         B         8
13      20_8C 20_8C_union_name.count         C         8
14      20_8D 20_8D_union_name.count         D         8
15      20_8E 20_8E_union_name.count         E         8
16      20_9A 20_9A_union_name.count         A         9
17      20_9B 20_9B_union_name.count         B         9
18      20_9C 20_9C_union_name.count         C         9
19      20_9D 20_9D_union_name.count         D         9
20      20_9E 20_9E_union_name.count         E         9

and I've runed DESeq2

dds=DESeqDataSetFromHTSeqCount(samplesDESeq,directory="directory/to/count/",design= ~replicate + condition)

after that, I analyzed it by DESeq function

dds <- DESeq(cds)

But, when I wanted compare everything with condition A, i cannot find conditionA in resultsNames

> resultsNames(dds)
[1] "Intercept"  "replicate3" "replicate7" "replicate8" "replicate9" "conditionB" "conditionC" "conditionD" "conditionE"

Where is a problem?

Thanks.

Answer 1

[Devon Ryan]

Condition A is the intercept.