Hi, Your sample sheet shows the same filename for "Reads" and "Peaks", which is unlikely to be right. The "Peaks" file should be the output of the peak caller (the peaks that MACS called); the "Reads" file should be the aligned reads, i.e. the *input* to the peak caller (the output of the alignment stage). Let me know if that fixes the problem. It should give an informative error message, though... I'll add that to the to-do list. Cheers, - Gord >--------------------------------------------------------------------- - > >Message: 1 >Date: Wed, 19 Dec 2012 16:17:07 +0100 >From: jluis.lavin at unavarra.es >To: bioconductor at r-project.org >Subject: [BioC] Diffbind error >Message-ID: > <e6a0d8855033e937b5236f5787e1d78d.squirrel at="" webmail.unavarra.es=""> >Content-Type: text/plain;charset=iso-8859-1 > >Dear list, > >--I'm trying to use Diffbind package to analyze some samples from a ChIP >seq experiment. >--I created a .csv samplesheet with the following fields and which samples >to analyze: > >SampleID Tissue Factor Condition Replicate Reads Control Peaks > >Chip_K27.1+ Neural K27 Responsive 1 Chip_K27.BED Input_K.BED Chip_K27.BED > >Chip_K27.2+ Neural K27 Responsive 1 Chip_K27d.BED Input_K.BED >Chip_K27d.BED > >--All my BED files have 6 lines and have been retrieved from MACS peak >caller. > >--When Diffbind reads the sheet everything seems correct: > >> chippy = dba(sampleSheet="Peaksets_sample_sheet.csv") > >Chip_K27.1+ Neural K27 Responsive 1 raw >Chip_K27.2+ Neural K27 Responsive 1 raw > >#it plots the correlation heatmap > >> plot(chippy) > >#But fails in this step after a while >> chippy = dba.count(chippy, minOverlap=3) > >Error in read.table(fn, skip = skipnum) : no lines available in input > >#Alternatively if I try this command >> chippy = dba.count(chippy) > >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 > >Would any of you shed any light on this issue? > >Best wishes and thanks in advance > >JL > > >> sessionInfo() >R version 2.15.1 (2012-06-22) >Platform: x86_64-redhat-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_1.4.0 Biobase_2.18.0 GenomicRanges_1.10.5 >[4] IRanges_1.16.4 BiocGenerics_0.4.0 BiocInstaller_1.8.3 > >loaded via a namespace (and not attached): > [1] amap_0.8-7 edgeR_3.0.7 gdata_2.12.0 >gplots_2.11.0 > [5] gtools_2.7.0 limma_3.14.3 RColorBrewer_1.0-5 >stats4_2.15.1 > [9] tools_2.15.1 zlibbioc_1.4.0 > > >-- >Dr. Jos? Luis Lav?n Trueba > >Dpto. de Producci?n Agraria >Grupo de Gen?tica y Microbiolog?a >Universidad P?blica de Navarra >31006 Pamplona >Navarra >SPAIN

Thank you Gordon, it was my mistake, I missunderstood the sample sheet and didn't create mine correctly. I think the packege is very very useful and I can't wait to see it working correctly with my samples ;) Best wishes JL El Jue, 20 de Diciembre de 2012, 12:17, Gordon Brown escribi?: > Hi, > > Your sample sheet shows the same filename for "Reads" and "Peaks", which > is unlikely to be right. The "Peaks" file should be the output of the > peak caller (the peaks that MACS called); the "Reads" file should be the > aligned reads, i.e. the *input* to the peak caller (the output of the > alignment stage). Let me know if that fixes the problem. > > It should give an informative error message, though... I'll add that to > the to-do list. > > Cheers, > > - Gord > > >>-------------------------------------------------------------------- -- >> >>Message: 1 >>Date: Wed, 19 Dec 2012 16:17:07 +0100 >>From: jluis.lavin at unavarra.es >>To: bioconductor at r-project.org >>Subject: [BioC] Diffbind error >>Message-ID: >> <e6a0d8855033e937b5236f5787e1d78d.squirrel at="" webmail.unavarra.es=""> >>Content-Type: text/plain;charset=iso-8859-1 >> >>Dear list, >> >>--I'm trying to use Diffbind package to analyze some samples from a ChIP >>seq experiment. >>--I created a .csv samplesheet with the following fields and which >> samples >>to analyze: >> >>SampleID Tissue Factor Condition Replicate Reads Control Peaks >> >>Chip_K27.1+ Neural K27 Responsive 1 Chip_K27.BED Input_K.BED >> Chip_K27.BED >> >>Chip_K27.2+ Neural K27 Responsive 1 Chip_K27d.BED Input_K.BED >>Chip_K27d.BED >> >>--All my BED files have 6 lines and have been retrieved from MACS peak >>caller. >> >>--When Diffbind reads the sheet everything seems correct: >> >>> chippy = dba(sampleSheet="Peaksets_sample_sheet.csv") >> >>Chip_K27.1+ Neural K27 Responsive 1 raw >>Chip_K27.2+ Neural K27 Responsive 1 raw >> >>#it plots the correlation heatmap >> >>> plot(chippy) >> >>#But fails in this step after a while >>> chippy = dba.count(chippy, minOverlap=3) >> >>Error in read.table(fn, skip = skipnum) : no lines available in input >> >>#Alternatively if I try this command >>> chippy = dba.count(chippy) >> >>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 >> >>Would any of you shed any light on this issue? >> >>Best wishes and thanks in advance >> >>JL >> >> >>> sessionInfo() >>R version 2.15.1 (2012-06-22) >>Platform: x86_64-redhat-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_1.4.0 Biobase_2.18.0 GenomicRanges_1.10.5 >>[4] IRanges_1.16.4 BiocGenerics_0.4.0 BiocInstaller_1.8.3 >> >>loaded via a namespace (and not attached): >> [1] amap_0.8-7 edgeR_3.0.7 gdata_2.12.0 >>gplots_2.11.0 >> [5] gtools_2.7.0 limma_3.14.3 RColorBrewer_1.0-5 >>stats4_2.15.1 >> [9] tools_2.15.1 zlibbioc_1.4.0 >> >> >>-- >>Dr. Jos? Luis Lav?n Trueba >> >>Dpto. de Producci?n Agraria >>Grupo de Gen?tica y Microbiolog?a >>Universidad P?blica de Navarra >>31006 Pamplona >>Navarra >>SPAIN > > -- Dr. Jos? Luis Lav?n Trueba Dpto. de Producci?n Agraria Grupo de Gen?tica y Microbiolog?a Universidad P?blica de Navarra 31006 Pamplona Navarra SPAIN