Loading sample sheet in DiffBind

Question

[nalewis]

I've been trying to solve this problem for a while now and I can't figure it out. I'm trying to run DiffBind on ATACseq samples I have and keep getting the following error after trying to create the dba:

line13 <- dba(sampleSheet="/home/nalewis/13lineATACseq/DiffBind/XIII_Line_Sheet.csv")
N13P1 DIPGK27M None Mut none 1 bed
N13P2 DIPGK27M None Mut none 2 bed
N13W1 DIPGWT None WT none 1 bed 
N13W2 DIPGWT None WT none 2 bed
Error in if (res >= minval) { : missing value where TRUE/FALSE needed

I've tried setting the minOverlap=2 and that did not solve my problem. I think the csv is fine because it reads my table just fine (see below for reference). It's just when I try to create the dba object that it suddenly throws an error at me and I haven't found a solution anywhere.

     samples <- read.csv("/home/nalewis/13lineATACseq/DiffBind/XIII_Line_Sheet.csv")
    > names(samples)
     [1] "SampleID"    "Tissue"      "Factor"      "Condition"   "Treatment"  
     [6] "Replicate"   "bamReads"    "Peaks"       "PeakCaller"  "PeakFormat" 
    [11] "ScoreCol"    "LowerBetter"
samples
  SampleID   Tissue Factor Condition Treatment Replicate
1    N13P1 DIPGK27M   None       Mut      none         1
2    N13P2 DIPGK27M   None       Mut      none         2
3    N13W1   DIPGWT   None        WT      none         1
4    N13W2   DIPGWT   None        WT      none         2
                                                   bamReads
1 /home/nalewis/13lineATACseq/alignment/N13P1/noM_N13P1.bam
2 /home/nalewis/13lineATACseq/alignment/N13P2/noM_N13P2.bam
3 /home/nalewis/13lineATACseq/alignment/N13W1/noM_N13W1.bam
4 /home/nalewis/13lineATACseq/alignment/N13W2/noM_N13W2.bam
                                                   Peaks PeakCaller PeakFormat
1 /home/nalewis/13lineATACseq/peaks/N13P1/N13P1peaks.bed        bed        bed
2 /home/nalewis/13lineATACseq/peaks/N13P2/N13P2peaks.bed        bed        bed
3 /home/nalewis/13lineATACseq/peaks/N13W1/N13W1peaks.bed       bed         bed
4 /home/nalewis/13lineATACseq/peaks/N13W2/N13W2peaks.bed        bed        bed
  ScoreCol LowerBetter
1        5       FALSE
2        5       FALSE
3        5       FALSE
4        5       FALSE

[Rory Stark]

What version of DiffBind are you running?

[nalewis]

I have bioconductor-diffbind version 1.16.3 through the build channel bioconda.

[Rory Stark]

Wow, are you sure? That is five years old and definitely no longer supported. What version of R are you running? Could you post the output of sessionInfo()?

[nalewis]

I have R 3.2.2. I was having issues checking the version of DiffBind the way the bioconductor website tells you to do it so I have gone to wrong place or entered the wrong code. I'm very new to coding so I'm still learning the ropes with all this. Here is the output from sessionInfo():

sessionInfo()

R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

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=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] DiffBind_1.16.3            RSQLite_1.0.0             
 [3] DBI_0.3.1                  locfit_1.5-9.1            
 [5] GenomicAlignments_1.6.3    Rsamtools_1.22.0          
 [7] Biostrings_2.38.4          XVector_0.10.0            
 [9] limma_3.28.10              SummarizedExperiment_1.0.2
[11] Biobase_2.32.0             GenomicRanges_1.22.4      
[13] GenomeInfoDb_1.6.3         IRanges_2.4.8             
[15] S4Vectors_0.8.11           BiocGenerics_0.18.0       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.2             lattice_0.20-33         GO.db_3.2.2            
 [4] gtools_3.5.0            digest_0.6.9            plyr_1.8.3             
 [7] futile.options_1.0.0    BatchJobs_1.6           ShortRead_1.28.0       
[10] ggplot2_2.1.0           gplots_2.17.0           zlibbioc_1.16.0        
[13] GenomicFeatures_1.22.13 annotate_1.50.0         gdata_2.17.0           
[16] Matrix_1.2-2            checkmate_1.6.3         systemPipeR_1.4.8      
[19] GOstats_2.36.0          splines_3.2.2           BiocParallel_1.4.3     
[22] stringr_1.0.0           pheatmap_1.0.8          RCurl_1.95-4.7         
[25] biomaRt_2.28.0          munsell_0.4.2           sendmailR_1.2-1        
[28] rtracklayer_1.30.1      base64enc_0.1-3         BBmisc_1.9             
[31] fail_1.3                edgeR_3.14.0            XML_3.98-1.3           
[34] AnnotationForge_1.12.2  bitops_1.0-6            grid_3.2.2             
[37] RBGL_1.46.0             xtable_1.8-0            GSEABase_1.32.0        
[40] gtable_0.1.2            magrittr_1.5            scales_0.3.0           
[43] graph_1.48.0            KernSmooth_2.23-15      amap_0.8-14            
[46] stringi_1.0-1           hwriter_1.3.2           genefilter_1.52.1      
[49] latticeExtra_0.6-26     futile.logger_1.4.1     brew_1.0-6             
[52] rjson_0.2.15            lambda.r_1.1.7          RColorBrewer_1.1-2     
[55] tools_3.2.2             Category_2.36.0         survival_2.38-3        
[58] AnnotationDbi_1.32.3    colorspace_1.2-6        caTools_1.17.1

Answer 1

[Rory Stark]

This a a 5-year old R environment, and no longer supported.

If you download an install a recent version of R (4.0 or greater) at https://www.r-project.org/, you can follow the Bioconductor installation instructions and get a workable environment fairly straightforwardly. I'd be happy to support your efforts with DiffBind using the current version.

[nalewis]

Ah I updated my R and everything is working! Thank you!