Hello Chinh- There are a couple of things going on here. First, there is an error in the documentation. The final column name is "fPeakFormat". The initial "f" is the problem, it should just be "PeakFormat" -- I'm not sure how the "f" snuck into the doc but I'll fix that. However, it should just be ignored, and your specification of peakFormat="bed" should override that. For "bed" format, the score should be in the fifth column of the peak file. Can you send me at least one of the peak files (Ptf1a- 2_1p6_090903peaks.bed.gz), or better all four, so I can see why this is being mis-parsed? Cheers- Rory From: Chinh Hoan <chinh.hoang@utsouthwestern.edu<mailto:chinh.hoang@u tsouthwestern.edu="">> Date: Mon, 10 Feb 2014 21:22:31 +0000 To: Rory Stark <rory.stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>> Subject: DiffBind loading Problem Dear Rory and Gordon, I would like to use DiffBind to compare my ChIPseq data in which I have two different antibodies against the same transcription factor named Ptf1a (2 replicates for each antibody). I want to get undifferentiated peaks between the two antibodies. I either putted the bowtie (Froma Bowtie) files or bedgraph files (from HMOER) into the bamReads and bamControl and the bed (peaks) files from MACS14 into Peaks. I attached the csv file with this mail. when I used Ptf1a = dba(sampleSheet="newPtf1a.csv") or Ptf1a = dba(sampleSheet="newPtf1a.csv", peakFormat="bed"), it warms me that Ptf1aJ2 Pancreas Ptf1a Jane 1 raw Ptf1aJ7 Pancreas Ptf1a Jane 2 raw Ptf1as4 Pancreas Ptf1a Mac 1 raw Ptf1as5 Pancreas Ptf1a Mac 2 raw Error in if (res >= minval) { : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors 2: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors 3: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors I don't know what I did wrong. Could you please give me your advise? thanks Chinh ________________________________________ UT Southwestern Medical Center The future of medicine, today. [[alternative HTML version deleted]]

Hi Chinh- Can you send along a sessionInfo() so I know what version you are using? When I use the original samplesheet you sent, with the peak files you send (five-column), and make the call you made, it builds the DBA object OK: > Ptf1a = dba(sampleSheet="newPtf1a.csv", peakFormat="bed") Ptf1aJ2 Pancreas Ptf1a Jane 1 raw Ptf1aJ7 Pancreas Ptf1a Jane 2 raw Ptf1as4 Pancreas Ptf1a Mac 1 raw Ptf1as5 Pancreas Ptf1a Mac 2 raw > Ptf1a 4 Samples, 22023 sites in matrix (33887 total): ID Tissue Factor Condition Replicate Peak.caller Intervals 1 Ptf1aJ2 Pancreas Ptf1a Jane 1 raw 19859 2 Ptf1aJ7 Pancreas Ptf1a Jane 2 raw 17561 3 Ptf1as4 Pancreas Ptf1a Mac 1 raw 24165 4 Ptf1as5 Pancreas Ptf1a Mac 2 raw 24404 When you called dba.count, were you using the BAM files or the bedgraph? Because DiffBind does not support bedgraph files, only BAM and BED. Cheers- Rory From: Chinh Hoan <chinh.hoang@utsouthwestern.edu<mailto:chinh.hoang@ut southwestern.edu="">> Date: Tue, 11 Feb 2014 16:32:59 +0000 To: Rory Stark <rory.stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>> Subject: RE: DiffBind loading Problem Hi Rory, Thanks for your quick response. Attached is the peak files with that I could not load with dba, but when I removed the fourth colunms i.,e the the scores are now on the fpurth colunm i can load with Ptf1a = dba(sampleSheet="newPtf1a.csv") but when I used Ptf1a = dba.count (Ptf1a) it said Error in cond$counts : $ operator is invalid for atomic vectors In addition: Warning message: In mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive = TRUE) : all scheduled cores encountered errors in user code. Chinh ________________________________ From: Rory Stark [Rory.Stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>] Sent: Tuesday, February 11, 2014 9:46 AM To: Chinh Hoan Cc: bioconductor@r-project.org<mailto:bioconductor@r-project.org> Subject: Re: DiffBind loading Problem Hello Chinh- There are a couple of things going on here. First, there is an error in the documentation. The final column name is "fPeakFormat". The initial "f" is the problem, it should just be "PeakFormat" -- I'm not sure how the "f" snuck into the doc but I'll fix that. However, it should just be ignored, and your specification of peakFormat="bed" should override that. For "bed" format, the score should be in the fifth column of the peak file. Can you send me at least one of the peak files (Ptf1a- 2_1p6_090903peaks.bed.gz), or better all four, so I can see why this is being mis-parsed? Cheers- Rory From: Chinh Hoan <chinh.hoang@utsouthwestern.edu<mailto:chinh.hoang@u tsouthwestern.edu="">> Date: Mon, 10 Feb 2014 21:22:31 +0000 To: Rory Stark <rory.stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>> Subject: DiffBind loading Problem Dear Rory and Gordon, I would like to use DiffBind to compare my ChIPseq data in which I have two different antibodies against the same transcription factor named Ptf1a (2 replicates for each antibody). I want to get undifferentiated peaks between the two antibodies. I either putted the bowtie (Froma Bowtie) files or bedgraph files (from HMOER) into the bamReads and bamControl and the bed (peaks) files from MACS14 into Peaks. I attached the csv file with this mail. when I used Ptf1a = dba(sampleSheet="newPtf1a.csv") or Ptf1a = dba(sampleSheet="newPtf1a.csv", peakFormat="bed"), it warms me that Ptf1aJ2 Pancreas Ptf1a Jane 1 raw Ptf1aJ7 Pancreas Ptf1a Jane 2 raw Ptf1as4 Pancreas Ptf1a Mac 1 raw Ptf1as5 Pancreas Ptf1a Mac 2 raw Error in if (res >= minval) { : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors 2: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors 3: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors I don't know what I did wrong. Could you please give me your advise? thanks Chinh ________________________________________ UT Southwestern Medical Center The future of medicine, today. [[alternative HTML version deleted]]