Yes, I extended the detail with which you can specify a peak file format in 2.6; as a result it is a bit fussier, if more flexible in the range of formats. I do apologize for the lack of backward compatibility in this particular case! -Rory ________________________________________ From: Gordon Brown Sent: 19 June 2013 17:23 To: Lawson, Nathan Cc: bioconductor at r-project.org; Rory Stark Subject: Re: error loading dba in DiffBind Hi, Turns out your sample sheet doesn't specify the peak format or peak caller. If you try again with: > x = dba(sampleSheet='AVbothChr6.csv',peakFormat='bed') you should be able to create the DBA object. The surprising thing is that it worked as-is in R 2.15. Maybe Rory changed the default peak format... not sure. Anyway, let me know if you have further trouble. Cheers, - Gord On 2013-06-19 16:51, "Lawson, Nathan" <nathan.lawson at="" umassmed.edu=""> wrote: > >Gord, > >Thanks for the quick reply. > >Attached is a .zip file with all of the peaksets (they are not so big >since they are only from one chromosome) and the sample sheet file. > >Below is session info from our cluster as well as from my computer (this >is a run from the terminal, but I have also run it with the R64 GUI >console with no problem). > > > >Session info from HPCC cluster: > >> sessionInfo() >R version 3.0.1 (2013-05-16) >Platform: x86_64-unknown-linux-gnu (64-bit) > >locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C >[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > >attached base packages: >[1] parallel stats graphics grDevices utils datasets methods >[8] base > >other attached packages: >[1] DiffBind_1.6.2 Biobase_2.20.0 GenomicRanges_1.12.4 >[4] IRanges_1.18.1 BiocGenerics_0.6.0 > >loaded via a namespace (and not attached): >[1] amap_0.8-7 edgeR_3.2.3 gdata_2.12.0.2 >gplots_2.11.0.1 >[5] gtools_2.7.1 limma_3.16.5 RColorBrewer_1.0-5 stats4_3.0.1 > >[9] zlibbioc_1.6.0 > > > > >session info from my computer: > >> sessionInfo() >R version 2.15.1 (2012-06-22) >Platform: i386-apple-darwin9.8.0/i386 (32-bit) > >locale: >[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >attached base packages: >[1] stats graphics grDevices utils datasets methods base > >other attached packages: >[1] DiffBind_1.4.2 Biobase_2.18.0 GenomicRanges_1.10.7 >[4] IRanges_1.16.6 BiocGenerics_0.4.0 > >loaded via a namespace (and not attached): > [1] amap_0.8-7 edgeR_3.0.8 gdata_2.12.0 >gplots_2.11.0 > [5] gtools_2.7.1 limma_3.14.4 parallel_2.15.1 >RColorBrewer_1.0-5 > [9] stats4_2.15.1 zlibbioc_1.4.0 > > > > > > > > > >Thanks, >Nathan > >On Jun 19, 2013, at 11:24 AM, Gordon Brown <gordon.brown at="" cruk.cam.ac.uk=""> >wrote: > >> Hi, Nathan, >> >> I haven't seen messages like these. The warnings suggest that numbers >>are >> being interpreted as strings, and converted to factors, but I can't >> imagine why that would happen. Can you send along your sample sheet, >>and >> the first few lines of your peaks files? I'll see if I can reproduce >>it. >> Also, can you let me know the sessionInfo() and operating system and >> version from both your computer and cluster? >> >> In case it helps, "dba.count" now has a "bLowMem" option that greatly >> reduces memory usage in dba.count; perhaps you will be able to get >>further >> on your local machine using that option. You'll have to upgrade to R >> 3.0.1/Bioconductor 2.12 though. >> >> Cheers, >> >> - Gord >> >> On 2013-06-19 15:23, "Lawson, Nathan" <nathan.lawson at="" umassmed.edu=""> >>wrote: >> >>> >>> I am using DiffBind to identify differentially occupied elements from >>> histone modification ChIP-Seq between two different cell lines. >>> >>> I successfully ran the package on my own computer with peaks and mapped >>> reads limited to a single human chromosome as a test. The analysis ran >>> nicely and the results looked good. Unfortunately, I was not able to >>>run >>> a full genome-wide analysis due to computational and space limitations. >>> Therefore, I tried to run the analysis on our high performance >>>computing >>> cluster, which is when the error appeared. >>> >>> When running the SAME EXACT set of files, including the same sample >>> sheet, on our cluster, I get the following error output, as well as >>> additional warnings that I have not seen previously: >>> >>>> AV = dba(sampleSheet="AVbothChr6.csv") >>> A1.0 HUAEC K27ac artery 1 raw >>> A1.1 HUAEC K27ac artery 2 raw >>> V1.0 HUVEC K27ac vein 1 raw >>> V1.1 HUVEC K27ac vein 2 raw >>> A1.2 HUAEC p300 artery 1 raw >>> A1.3 HUAEC p300 artery 2 raw >>> V1.3 HUVEC p300 vein 1 raw >>> V2.6 HUVEC p300 vein 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 >>> 4: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>> 5: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>> 6: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>> 7: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>> 8: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>>> >>> >>> >>> Again, these datasets were successfully entered as a dba object and >>> subsequently analyzed using DiffBind on my computer. The original >>>input >>> files were simply transferred to the cluster to re-test there. The >>>only >>> difference (I can see) is that the cluster is currently running R-3.0.1 >>> and I was running 2.15. >>> >>> I also tried making the peaks.bed files into a 6-column format (the >>> original bed files only had 5 columns), but this did not seem to solve >>> the problem. >>> >>> Any suggestions are welcome. >>> >>> Thanks, >>> Nathan >>> >>> Nathan D. Lawson, Ph.D. >>> Associate Professor >>> Program in Gene Function and Expression >>> University of Massachusetts Medical School >>> 364 Plantation Street >>> LRB617 >>> Worcester, MA 01605 >>> website: lawsonlab.umassmed.edu >>> email: nathan.lawson at umassmed.edu >>> phone: 508-856-1177 >>> >> > > >

Gord, Excellent! That did the trick. Thanks for your help. Thanks, Nathan On Jun 19, 2013, at 12:23 PM, Gordon Brown <gordon.brown at="" cruk.cam.ac.uk=""> wrote: > Hi, > > Turns out your sample sheet doesn't specify the peak format or peak > caller. If you try again with: > >> x = dba(sampleSheet='AVbothChr6.csv',peakFormat='bed') > > you should be able to create the DBA object. The surprising thing is that > it worked as-is in R 2.15. Maybe Rory changed the default peak format... > not sure. > > Anyway, let me know if you have further trouble. > > Cheers, > > - Gord > > > On 2013-06-19 16:51, "Lawson, Nathan" <nathan.lawson at="" umassmed.edu=""> wrote: > >> >> Gord, >> >> Thanks for the quick reply. >> >> Attached is a .zip file with all of the peaksets (they are not so big >> since they are only from one chromosome) and the sample sheet file. >> >> Below is session info from our cluster as well as from my computer (this >> is a run from the terminal, but I have also run it with the R64 GUI >> console with no problem). >> >> >> >> Session info from HPCC cluster: >> >>> sessionInfo() >> R version 3.0.1 (2013-05-16) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] DiffBind_1.6.2 Biobase_2.20.0 GenomicRanges_1.12.4 >> [4] IRanges_1.18.1 BiocGenerics_0.6.0 >> >> loaded via a namespace (and not attached): >> [1] amap_0.8-7 edgeR_3.2.3 gdata_2.12.0.2 >> gplots_2.11.0.1 >> [5] gtools_2.7.1 limma_3.16.5 RColorBrewer_1.0-5 stats4_3.0.1 >> >> [9] zlibbioc_1.6.0 >> >> >> >> >> session info from my computer: >> >>> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] DiffBind_1.4.2 Biobase_2.18.0 GenomicRanges_1.10.7 >> [4] IRanges_1.16.6 BiocGenerics_0.4.0 >> >> loaded via a namespace (and not attached): >> [1] amap_0.8-7 edgeR_3.0.8 gdata_2.12.0 >> gplots_2.11.0 >> [5] gtools_2.7.1 limma_3.14.4 parallel_2.15.1 >> RColorBrewer_1.0-5 >> [9] stats4_2.15.1 zlibbioc_1.4.0 >> >> >> >> >> >> >> >> >> >> Thanks, >> Nathan >> >> On Jun 19, 2013, at 11:24 AM, Gordon Brown <gordon.brown at="" cruk.cam.ac.uk=""> >> wrote: >> >>> Hi, Nathan, >>> >>> I haven't seen messages like these. The warnings suggest that numbers >>> are >>> being interpreted as strings, and converted to factors, but I can't >>> imagine why that would happen. Can you send along your sample sheet, >>> and >>> the first few lines of your peaks files? I'll see if I can reproduce >>> it. >>> Also, can you let me know the sessionInfo() and operating system and >>> version from both your computer and cluster? >>> >>> In case it helps, "dba.count" now has a "bLowMem" option that greatly >>> reduces memory usage in dba.count; perhaps you will be able to get >>> further >>> on your local machine using that option. You'll have to upgrade to R >>> 3.0.1/Bioconductor 2.12 though. >>> >>> Cheers, >>> >>> - Gord >>> >>> On 2013-06-19 15:23, "Lawson, Nathan" <nathan.lawson at="" umassmed.edu=""> >>> wrote: >>> >>>> >>>> I am using DiffBind to identify differentially occupied elements from >>>> histone modification ChIP-Seq between two different cell lines. >>>> >>>> I successfully ran the package on my own computer with peaks and mapped >>>> reads limited to a single human chromosome as a test. The analysis ran >>>> nicely and the results looked good. Unfortunately, I was not able to >>>> run >>>> a full genome-wide analysis due to computational and space limitations. >>>> Therefore, I tried to run the analysis on our high performance >>>> computing >>>> cluster, which is when the error appeared. >>>> >>>> When running the SAME EXACT set of files, including the same sample >>>> sheet, on our cluster, I get the following error output, as well as >>>> additional warnings that I have not seen previously: >>>> >>>>> AV = dba(sampleSheet="AVbothChr6.csv") >>>> A1.0 HUAEC K27ac artery 1 raw >>>> A1.1 HUAEC K27ac artery 2 raw >>>> V1.0 HUVEC K27ac vein 1 raw >>>> V1.1 HUVEC K27ac vein 2 raw >>>> A1.2 HUAEC p300 artery 1 raw >>>> A1.3 HUAEC p300 artery 2 raw >>>> V1.3 HUVEC p300 vein 1 raw >>>> V2.6 HUVEC p300 vein 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 >>>> 4: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>>> 5: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>>> 6: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>>> 7: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>>> 8: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors >>>>> >>>> >>>> >>>> Again, these datasets were successfully entered as a dba object and >>>> subsequently analyzed using DiffBind on my computer. The original >>>> input >>>> files were simply transferred to the cluster to re-test there. The >>>> only >>>> difference (I can see) is that the cluster is currently running R-3.0.1 >>>> and I was running 2.15. >>>> >>>> I also tried making the peaks.bed files into a 6-column format (the >>>> original bed files only had 5 columns), but this did not seem to solve >>>> the problem. >>>> >>>> Any suggestions are welcome. >>>> >>>> Thanks, >>>> Nathan >>>> >>>> Nathan D. Lawson, Ph.D. >>>> Associate Professor >>>> Program in Gene Function and Expression >>>> University of Massachusetts Medical School >>>> 364 Plantation Street >>>> LRB617 >>>> Worcester, MA 01605 >>>> website: lawsonlab.umassmed.edu >>>> email: nathan.lawson at umassmed.edu >>>> phone: 508-856-1177 >>>> >>> >> >> >> >