I am doing a DESeq2 comparison with different levels and one factor. To do this, I have performed the analysis in two different ways.

First, putting all the samples in the same DESeq object and then extracting each comparison:

> sampleinfo
    FileName    SampleName  Status
    A_1_count   A_1 A       
    A_2_count   A_2 A       
    B_3_count   B_3 B       
    B_4_count   B_4 B       
    C_5_count   C_5 C   
    C_6_count   C_6 C   
    D_7_count   D_7 D   
    D_8_count   D_8 D   
    E_9_count   E_9 E   
    E_10_count  E_10    E

dds <- DESeqDataSetFromMatrix(countData = cts,
                                colData = sampleinfo,
                              design = ~ Status)

dds$Status <- relevel(dds$Status, ref = "E")

And the results:

dds <- DESeq(dds)
res_A <- results(dds,name="Status_A_vs_E")
res_B <- results(dds,name="Status_B_vs_E")
res_C <- results(dds,name="Status_C_vs_E")
res_D <- results(dds,name="Status_D_vs_E")

And doing these comparisons one by one separately on different DESeq objects.

> sampleinfo_A
    FileName    SampleName  Status
    A_1_count   A_1 A       
    A_2_count   A_2 A       
    E_9_count   E_9 E   
    E_10_count  E_10    E

> sampleinfo_B
    FileName    SampleName  Status
    B_3_count   B_3 B       
    B_4_count   B_4 B       
    E_9_count   E_9 E   
    E_10_count  E_10    E

dds_A <- DESeqDataSetFromMatrix(countData = cts_A,
                                colData = sampleinfo_A,
                              design = ~ Status)

dds_B <- DESeqDataSetFromMatrix(countData = cts_B,
                                colData = sampleinfo_B,
                              design = ~ Status)

And the results:

dds_A <- DESeq(dds_A)
res_A <- results(dds_A)

dds_B <- DESeq(dds_B)
res_B <- results(dds_B)

(Repeat for each condition)

However, the results give me different between the 2 methods. Does anyone know why is this happening? How it is the correct way to compare all to E?

Thank you!