I have 6 samples from 3 conditions with two replicates for each condition and I want to make a comparison of these conditions amongst each other. Here is the sample info:

 SampleID         Factor    Condtion     Replicate PeakCaller
1       Mel239_1   CTCF      Mel239         1 narrowPeak
2       Mel239_2   CTCF      Mel239         2 narrowPeak
3 Mel_Braf_res_1   CTCF MelBraf_res         1 narrowPeak
4 Mel_Braf_res_2   CTCF MelBraf_res         2 narrowPeak
5  Mel_Mek_res_1   CTCF  MelMek_res         1 narrowPeak
6  Mel_Mek_res_2   CTCF  MelMek_res         2 narrowPeak
                  bamReads      ControlID
1 Bam/SKMel239_CTCF_1.mLb.clN.sorted.bam      Input_Mel
2 Bam/SKMel239_CTCF_2.mLb.clN.sorted.bam      Input_Mel
3 Bam/SKMel6WC_1.mLb.clN.sorted.bam Input_Braf_res
4 Bam/SKMel6WC_2.mLb.clN.sorted.bam Input_Braf_res
5 Bam/SKMel2xTD_1.mLb.clN.sorted.bam Input_Meki_res
6 Bam/SKMel2xTD_2.mLb.clN.sorted.bam Input_Meki_res
                     bamControl
1  Bam/SKMel239_Input_1.mLb.clN.sorted.bam
2 Bam/SKMel239_Input_1.mLb.clN.sorted.bam
3 Bam/SKMel6WC_Input_1.mLb.clN.sorted.bam
4 Bam/SKMel6WC_Input_1.mLb.clN.sorted.bam
5 Bam/SKMel2xTD_Input_1.mLb.clN.sorted.bam
6 Bam/SKMel2xTD_Input_1.mLb.clN.sorted.bam
                            Peaks      Tissue
1 Peaks/SKMel239_CTCF_1_peaks.narrowPeak      Mel239
2 Peaks/SKMel239_CTCF_2_peaks.narrowPeak      Mel239
3 Peaks/SKMel6WC_1_peaks.narrowPeak MelBraf_res
4 Peaks/SKMel6WC_2_peaks.narrowPeak MelBraf_res
5 Peaks/SKMel2xTD_1_peaks.narrowPeak  MelMek_res
6 Peaks/SKMel2xTD_2_peaks.narrowPeak  MelMek_res

Here is the code which I used:

DBdata <- DiffBind::dba(sampleSheet = samples)

DBdata <- DiffBind::dba.count(DBdata,summits = 250,bUseSummarizeOverlaps = TRUE)
DBdata <- DiffBind::dba.contrast(DBdata,minMembers = 2)
DBdata <- DiffBind::dba.analyze(DBdata)