Dear Bioconductor list.

I have 3 time points (conditions) and 4 replicates.
This is what my colDataTable looks like:
            condition       ind
B10    1_Uninfected    Ind_1
B11    1_Uninfected    Ind_1
B12    1_Uninfected    Ind_1
B20    1_Uninfected    Ind_2
B30    1_Uninfected    Ind_3
B40    1_Uninfected    Ind_4
B21    2_Peak_infection    Ind_2
B31    2_Peak_infection    Ind_3
B41    2_Peak_infection    Ind_4
B22    3_After_infection    Ind_2
B32    3_After_infection    Ind_3
B42    3_After_infection    Ind_4

(I had to add numbers in front of the treatments because otherwise deseq
would only test the first two groups against After_infection, but I was
also interested in the results from Peak vs Uninfected.)

dds <- DESeqDataSetFromMatrix(countData = counts,
                             colData = colDataTable,
                             design = ~ ind+condition)
dds <- DESeq(dds)
resultsNames(dds)
res <- results(dds, "condition_2_Peak_infection_vs_1_Uninfected")

This all works perfectly fine.
The problem is when I changed the number in the condition-names, so I could
change which group to test against, the result output from the test with
the exact same groups is different. I.e. if I change the name of the first
two conditions to: "2_Uninfected" and "1_Peak_infection", with calling upon
the results with:

res <- results(dds, "condition_2_Uninfected_vs_1_Peak_infection")

then my output is different from the first test between the exact same
groups. The baseMean remains exactly the same, but the other columns:
log2foldchange, p-value, and FDR is not. Why? I would expect only the
log2foldchange to switch symbols, and nothing else.

Can anyone explain if I'm doing something wrong or why deseq output
different results?
I'm using version DESeq2_1.0.9.

Thank you,
Elin.

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