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Question: error loading dba in DiffBind
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gravatar for Gord Brown
5.3 years ago by
Gord Brown570
United Kingdom
Gord Brown570 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 >
ADD COMMENTlink modified 5.3 years ago by Lawson, Nathan30 • written 5.3 years ago by Gord Brown570
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gravatar for Lawson, Nathan
5.3 years ago by
Lawson, Nathan30 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
ADD COMMENTlink written 5.3 years ago by Lawson, Nathan30
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5.3 years ago by
Lawson, Nathan30 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 >> >
ADD COMMENTlink written 5.3 years ago by Lawson, Nathan30
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gravatar for Gord Brown
5.3 years ago by
Gord Brown570
United Kingdom
Gord Brown570 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 >>> >> > > >
ADD COMMENTlink written 5.3 years ago by Gord Brown570
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 >>> >> > > >
ADD REPLYlink written 5.3 years ago by Rory Stark2.5k
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 >>>> >>> >> >> >> >
ADD REPLYlink written 5.3 years ago by Lawson, Nathan30
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