Hi Kasthuri-



You probably know that without replicates, this really isn't an appropriate way to do the analysis. I'll take a look to see if it is something obvious going wrong (I like to at least add more informative warnings), but in general we don't like to spend too much time getting these unreplicated analyses working.



The sample sheet and the function calls look OK. I'll need to examine the DBA object itself ("tamoxifen") -- can you share it with me (maybe on Dropbox, or via email if it is less than a few megabytes), saved (preferably using dba.save) after the call to dba.count?



Also, please send a sessionInfo() output so I can know the version of all the packages you have loaded.



Cheers-

Rory



________________________________
From: Kannan, Kasthuri [Kasthuri.Kannan@nyumc.org]
Sent: 14 December 2013 14:14
To: Gordon Brown; Rory Stark
Subject: DiffBind Error.

Dear Dr. Brown and Dr. Stark,

I am trying to use DiffBind and having an error. The data set is just two conditions without any replicates. I set up the contrast manually as groups as suggested.I get the error in dba.analyze step. Here is the actual commands and the error I get:

> tamoxifen = dba(sampleSheet="~/Data/NYU/Michael/Marcus/sample_info.csv")
S1 Neuronal GR Dex  1 MACS
S2 Neuronal GR BDNFDex  1 MACS
> tamoxifen = dba.count(tamoxifen, minOverlap=2)
> tamoxifen = dba.contrast(tamoxifen, tamoxifen$masks$Dex, tamoxifen$masks$BDNFDex,"Dex","BDNFDex")
> tamoxifen = dba.analyze(tamoxifen)
Error in d$span : $ operator is invalid for atomic vectors
In addition: Warning messages:
1: Some groups have no replicates. Results may be unreliable.
2: In estimateCommonDisp(res) :
  There is no replication, setting dispersion to NA.
3: In estimateGLMCommonDisp.default(y = y$counts, design = design,  :
  No residual df: setting dispersion to NA
4: In estimateGLMTagwiseDisp.default(y = y$counts, design = design,  :
  No residual df: setting dispersion to NA

Also, I am attaching the sample_info.csv that I use.

It will be great to get some assistance from you.

Thanks
Kasthuri

+++++++++++++++++++++++++++++++++
Kasthuri Kannan, PhD.
Assistant Professor of Pathology
Investigator, Genome Technology Center
New York University
Kasthuri.Kannan@nyumc.org | (646) 501 9909
+++++++++++++++++++++++++++++++++

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