Dear Rory, Merry Christmas! Thank you for replying in spite of being a holiday, and especially being in vacation. I truly appreciate it. I will use this feature to retrieve the information. Kind regards Kasthuri From: Rory Stark <rory.stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>> Date: Wednesday, December 25, 2013 2:53 PM To: "Kannan, Kasthuri S./Sloan-Kettering Institute" <kasthuri.kannan@nyumc.org<mailto:kasthuri.kannan@nyumc.org>> Cc: Gordon Brown <gordon.brown@cruk.cam.ac.uk<mailto:gordon.brown@cruk.cam.ac.uk>>, "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>> Subject: RE: DiffBind Error. Hi Kashthuri- The correlation values should be returned by the call to dba.plotHeatmap. The peak scores that are used to compute the correlations (normalized to 0...1 for peaks called for the sample, and set to -1 if the peak is not called for the sample) can be retrieved using dba.peakset and setting bRetrieve=TRUE. This will come back as a GRanges by default; you can get a data frame by setting DataType=DBA_DATA_FRAME. Cheers- Rory ________________________________ From: Kannan, Kasthuri [Kasthuri.Kannan@nyumc.org<mailto:kasthuri.kannan@nyumc.org>] Sent: 24 December 2013 22:50 To: Rory Stark Cc: Gordon Brown; bioconductor@r-project.org<mailto:bioconductor@r-project.org> Subject: Re: DiffBind Error. Dear Rory, Thanks again for the clarification. DiffBind is really proving to be useful in our analysis. I am wondering how does one get the numbers for the correlation heat map (using only the peaks data) instead of plotting it. This is the initial heat map that gets generated when we load the sample sheet. Any hints will be really useful. I am new to R as well, so my apologies if this too trivial. Thanks Kasthuri From: Rory Stark <rory.stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>> Date: Sunday, December 15, 2013 at 2:55 PM To: Kasthuri Kannan <kasthuri.kannan@nyumc.org<mailto:kasthuri.kannan@nyumc.org>> Cc: Gordon Brown <gordon.brown@cruk.cam.ac.uk<mailto:gordon.brown@cruk.cam.ac.uk>>, "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>> Subject: RE: DiffBind Error. 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<mailto: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. 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