Trying to set up a contrast based on some masks and having some problems. The dba.count looks as follows: 

12 Samples, 1054182 sites in matrix (2657422 total):

     ID Tissue Factor Condition Treatment Replicate Caller Intervals

1  MBV1  BN1     DR      MALE   VEHICLE         1 narrow    500000

2  MBV2  BN1     DR      MALE   VEHICLE         2 narrow    281265

3  MBV3  BN1     DR      MALE   VEHICLE         3 narrow    500000

4  FBV1  BN3     DR    FEMALE   VEHICLE         1 narrow    500000

5  FBV2  BN3     DR    FEMALE   VEHICLE         2 narrow    500000

6  FBV3  BN3     DR    FEMALE   VEHICLE         3 narrow    439016

7  MBE7  BN2     DR      MALE  TREATMENT         1 narrow    500000

8  MBE8  BN2     DR      MALE  TREATMENT         2 narrow    500000

9  MBE9  BN2     DR      MALE  TREATMENT         3 narrow    500000

10 FBE1  BN4     DR    FEMALE  TREATMENT         1 narrow    500000

11 FBE2  BN4     DR    FEMALE  TREATMENT         2 narrow    500000

12 FBE3  BN4     DR    FEMALE  TREATMENT         3 narrow    500000

I would like to set up a comparison where I pair male or female with vehicle or treatment. Have the following dba.masks written:

CHIP_adult_BN_mask_MaleVeh<-dba.mask(CHIP_adult_BN_count, attribute = DBA_CONDITION, DBA_TREATMENT, combine = "MALE and VEHICLE")
 CHIP_adult_BN_mask_FemaleVeh<-dba.mask(CHIP_adult_BN_count, attribute = DBA_CONDITION, DBA_TREATMENT, combine = "FEMALE and VEHICLE")
CHIP_adult_BN_mask_MaleTRE<-dba.mask(CHIP_adult_BN_count, attribute = DBA_CONDITION, DBA_TREATMENT, combine = "MALE and TREATMENT")
 CHIP_adult_BN_mask_FemaleTRE<-dba.mask(CHIP_adult_BN_count, attribute = DBA_CONDITION, DBA_TREATMENT, combine = "FEMALE and TREATMENT")

After this tried setting up the following dba.contrast prior to analysis: 

CHIP_adult_BN_Malecontrast<-dba.contrast(CHIP_adult_BN_count, group1 = CHIP_adult_BN_mask_MaleVeh, group2 = CHIP_adult_BN_mask_MaleTRE, minMembers = 3)

Error: Warning message:
Unable to add redundant contrast

Any ideas? Thanks!

The parameters in the calls to dba.mask() are incorrect. The attribute parameter is being set to DBA_CONDITION only; the third parameter, value, is being set to DBA_TREAMENT, which doesn't make sense, and combine should be set to one of "or", "and", "nor", or "nand".

There is a much easier way to accomplish what I think you are trying to do using the pre-defined masks: 

> masks <- CHIP_adult_BN_count$masks
> CHIP_adult_BN_mask_MaleVeh   <- masks$MALE & masks$VEHICLE
> CHIP_adult_BN_mask_FemaleVeh <- masks$FEMALE & masks$VEHICLE 
> CHIP_adult_BN_mask_MaleTRE   <- masks$MALE & masks$TREATMENT
> CHIP_adult_BN_mask_FemaleTRE <- masks$FEMALE & masks$TREATMENT
> CHIP_adult_BN_Malecontrast   <- 
      dba.contrast(CHIP_adult_BN_count, 
                   group1 = CHIP_adult_BN_mask_MaleVeh, 
                   group2 = CHIP_adult_BN_mask_MaleTRE)

You shouldn't use the minMembers parameter when  specifying contrasts, as this parameter is only used when contrasts are generated automatically.