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