[BioC] DiffBind error with DBA_DESEQ_GLM and warning with DBA_EDGE_GLM

[Elisabetta Manduchi]

Hello,
I'm using DiffBind version 1.2.0 with R 2.15.0 on linux.
I've created a dba object data.deseq and run:

> data.deseq =
dba.count(data.deseq,score=DBA_SCORE_TMM_READS_EFFECTIVE,bRemoveDuplicates=T,bCorPlot=F)
> data.deseq =
dba.contrast(data.deseq,categories=DBA_TISSUE,block=DBA_FACTOR)

So data.deseq looks like this:

24 Samples, 212418 sites in matrix:
     ID     Tissue Factor Condition Replicate Intervals
1   A2       Arch      2         M         1    212418
2   A3       Arch      3         F         2    212418
3   A4       Arch      4         M         3    212418
4   A5       Arch      5         F         4    212418
5   A7       Arch      7         F         5    212418
6   D2 Descending      2         M         1    212418
7   D3 Descending      3         F         2    212418
8   D4 Descending      4         M         3    212418
9   D5 Descending      5         F         4    212418
10  D7 Descending      7         F         5    212418
11 A10       Arch     10         F         6    212418
12 A11       Arch     11         M         7    212418
13 A12       Arch     12         M         8    212418
14 A13       Arch     13         M         9    212418
15 A14       Arch     14         M        10    212418
16 A15       Arch     15         F        11    212418
17 A17       Arch     17         F        12    212418
18 D10 Descending     10         F         6    212418
19 D11 Descending     11         M         7    212418
20 D12 Descending     12         M         8    212418
21 D13 Descending     13         M         9    212418
22 D14 Descending     14         M        10    212418
23 D15 Descending     15         F        11    212418
24 D17 Descending     17         F        12    212418

1 Contrast:
   Group1 Members1     Group2 Members2 Block1Val InBlock1 Block2Val InBlock2
1   Arch       12 Descending       12        10        2 11        2
   Block3Val InBlock3 Block4Val InBlock4 Block5Val InBlock5 Block6Val
InBlock6
1        12        2        13        2        14        2 15        2
   Block7Val InBlock7 Block8Val InBlock8 Block9Val InBlock9 Block10Val
InBlock10
1        17        2         2        2         3        2 4         2
   Block11Val InBlock11 Block12Val InBlock12
1          5         2          7         2


1. When I then try to run:
data.deseq =
dba.analyze(data.deseq,method=DBA_DESEQ_GLM,bSubControl=F,bCorPlot=F)

I get the following error:
Error in .local(object, ...) :
   None of your conditions is replicated. Use method='blind' to estimate
across conditions, or 'pooled-CR', if you have crossed factors.
In addition: Warning message:
Unable to use tagwise dispersion estimates with GLM

I'm not clear why it's not seeing the replicates, since I have 12 for
each of Arch and Descending. Am I setting things up incorrectly?

2. Note that I've also analyzed the same dba with method DBA_EDGER_GLM. This
ran, but gave me the following warning on which I'm unclear

Warning message:
In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence

and it only found 154 significant intervals out of the over 212000 input
sites, which seems too low.

Anybody can advice on the above? Thanks,
Elisabetta