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Question: DiffBind: Error in heights * sapply(called, function(x) x)
0
gravatar for zhaolin20042008
12 months ago by
U of Michigan
zhaolin200420080 wrote:

Hello, Rory, Thank you for suggestions at C: Warnings when update DiffBind and running errors. I still failed run with dba.count, however. Here is what I have done. 

1. I have update all the packages. when loading Diffbind 2.6, there is no warnings.

2. Then I run dba.count using  summits=150 with score default. the error came out again. How could I fix it? 

Error in heights * sapply(called, function(x) x) : non-conformable arrays

Many Thanks

Zhaolin 

> library(DiffBind)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: âBiocGenericsâ

The following objects are masked from âpackage:parallelâ:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from âpackage:statsâ:

    IQR, mad, sd, var, xtabs

The following objects are masked from âpackage:baseâ:

    anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
    colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: âS4Vectorsâ

The following object is masked from âpackage:baseâ:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: âmatrixStatsâ

The following objects are masked from âpackage:Biobaseâ:

    anyMissing, rowMedians


Attaching package: âDelayedArrayâ

The following objects are masked from âpackage:matrixStatsâ:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from âpackage:baseâ:

    apply

> eiff<-dba(sampleSheet="090217_3_CD4.csv",config=data.frame(RunParallel=TRUE, reportInit="eiff",AnalysisMethod=DBA_DESEQ2,th=0.05))
​>eiff1<-dba.count(eiff, minOverlap=12,summits=150,readFormat=DBA_READS_DEFAULT, bParallel=eiff$config$RunParallel)
Re-centering peaks...
Error in heights * sapply(called, function(x) x) : non-conformable arrays

> sessionInfo()

R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/lapack/liblapack.so.3.0

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] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] DiffBind_2.6.1             SummarizedExperiment_1.8.0
 [3] DelayedArray_0.4.1         matrixStats_0.52.2        
 [5] Biobase_2.38.0             GenomicRanges_1.30.0      
 [7] GenomeInfoDb_1.14.0        IRanges_2.12.0            
 [9] S4Vectors_0.16.0           BiocGenerics_0.24.0       

 

loaded via a namespace (and not attached):
 [1] Category_2.44.0          bitops_1.0-6             bit64_0.9-7             
 [4] RColorBrewer_1.1-2       progress_1.1.2           Rgraphviz_2.22.0        
 [7] tools_3.4.2              backports_1.1.1          R6_2.2.2                
[10] KernSmooth_2.23-15       DBI_0.7                  lazyeval_0.2.1          
[13] colorspace_1.3-2         prettyunits_1.0.2        RMySQL_0.10.13          
[16] bit_1.1-12               compiler_3.4.2           sendmailR_1.2-1         
[19] graph_1.56.0             rtracklayer_1.38.0       caTools_1.17.1          
[22] scales_0.5.0             checkmate_1.8.5          BatchJobs_1.7           
[25] genefilter_1.60.0        RBGL_1.54.0              stringr_1.2.0           
[28] digest_0.6.12            Rsamtools_1.30.0         AnnotationForge_1.20.0  
[31] XVector_0.18.0           base64enc_0.1-3          pkgconfig_2.0.1         
[34] limma_3.34.2             rlang_0.1.4              RSQLite_2.0             
[37] BBmisc_1.11              BiocInstaller_1.28.0     bindr_0.1               
[40] GOstats_2.44.0           hwriter_1.3.2            BiocParallel_1.10.1     
[43] gtools_3.5.0             dplyr_0.7.4              RCurl_1.95-4.8          
[46] magrittr_1.5             GO.db_3.5.0              GenomeInfoDbData_0.99.1 
[49] Matrix_1.2-12            Rcpp_0.12.14             munsell_0.4.3

[52] stringi_1.1.6            edgeR_3.18.1             zlibbioc_1.24.0         

[55] gplots_3.0.1             plyr_1.8.4               grid_3.4.2              
[58] blob_1.1.0               ggrepel_0.7.0            gdata_2.18.0            
[61] lattice_0.20-35          Biostrings_2.46.0        splines_3.4.2           
[64] GenomicFeatures_1.30.0   annotate_1.56.1          locfit_1.5-9.1          
[67] rjson_0.2.15             systemPipeR_1.12.0       biomaRt_2.34.0          
[70] glue_1.2.0               XML_3.98-1.9             ShortRead_1.36.0        
[73] latticeExtra_0.6-28      data.table_1.10.4-3      gtable_0.2.0            
[76] amap_0.8-14              assertthat_0.2.0         ggplot2_2.2.1           
[79] xtable_1.8-2             survival_2.41-3          tibble_1.3.4            
[82] pheatmap_1.0.8           GenomicAlignments_1.14.1 AnnotationDbi_1.40.0    
[85] memoise_1.1.0            bindrcpp_0.2             brew_1.0-6              
[88] GSEABase_1.40.1   

 

ADD COMMENTlink modified 17 days ago by Ashu10 • written 12 months ago by zhaolin200420080

Hi Zhaolin,

I ran into the same error message while running DiffBind. Did you happen to figure out the reason and/or a fix? 

Thanks for your help!

Ashu

ADD REPLYlink written 5 weeks ago by Ashu10
0
gravatar for Rory Stark
5 weeks ago by
Rory Stark2.6k
CRUK, Cambridge, UK
Rory Stark2.6k wrote:

I've been unable to reproduce this issue. Perhaps someone experiencing it can help by sending me an example where it occurs?

One thing to try would be to run the dba.count() call with summits=TRUE (instead of summits=150), then send me the resulting DBA object so I can have a look. I may be able to see what is going wrong with needing access to a bunch of bam files.

-Rory

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Rory Stark2.6k

 Hi Rory, 

I received the same error with dba.count() called with summits=25, it also seems to require significantly more memory. 

> DBA.count = dba.count(DBA, score = DBA_DESEQ2, bUseSummarizeOverlaps = FALSE, mapQCth = 30, bCorPlot = TRUE, bParallel = TRUE, minOverlap = 2, summits = 25, bRemoveDuplicates = TRUE, bScaleControl = TRUE)
Re-centering peaks...
Error in heights * sapply(called, function(x) x) : non-conformable arrays

I also attempted your suggestion with summits=TRUE instead and that seemed to work fine. 

> DBA.count = dba.count(DBA, score = DBA_DESEQ2, bUseSummarizeOverlaps = FALSE, mapQCth = 30, bCorPlot = TRUE, bParallel = TRUE, minOverlap = 2, summits = TRUE, bRemoveDuplicates = TRUE, bScaleControl = TRUE)

ADD REPLYlink modified 18 days ago • written 18 days ago by loretta0
0
gravatar for Ashu
17 days ago by
Ashu10
Ashu10 wrote:

Hi Rory,

It took me some time to get back on this, but here are the things you asked for:

data <- DiffBind::dba(sampleSheet = samples, peakFormat="narrow", scoreCol = 5, filter = 20, config=data.frame(RunParallel=TRUE) )
SampleA-tNKT-liver-a Unknown None SampleA NONE 1 narrow
SampleA-tNKT-liver-b Unknown None SampleA NONE 2 narrow
SampleA-tNKT-liver-c Unknown None SampleA NONE 3 narrow
SampleA-tNKT-liver-d Unknown None SampleA NONE 4 narrow
SampleB-tNKT-liver-a Unknown None SampleB NONE 1 narrow
SampleB-tNKT-liver-b Unknown None SampleB NONE 2 narrow
SampleB-tNKT-liver-c Unknown None SampleB NONE 3 narrow
SampleB-tNKT-liver-d Unknown None SampleB NONE 4 narrow
SampleC-tNKT-liver-a Unknown None SampleC NONE 1 narrow
SampleC-tNKT-liver-b Unknown None SampleC NONE 2 narrow
SampleC-tNKT-liver-c Unknown None SampleC NONE 3 narrow
SampleC-tNKT-liver-d Unknown None SampleC NONE 4 narrow

data
12 Samples, 29536 sites in matrix (34315 total):
                    ID  Tissue Factor Condition Treatment Replicate Caller
1  SampleA-tNKT-liver-a Unknown   None    SampleA      NONE         1 narrow
2  SampleA-tNKT-liver-b Unknown   None    SampleA      NONE         2 narrow
3  SampleA-tNKT-liver-c Unknown   None    SampleA      NONE         3 narrow
4  SampleA-tNKT-liver-d Unknown   None    SampleA      NONE         4 narrow
5  SampleB-tNKT-liver-a Unknown   None    SampleB      NONE         1 narrow
6  SampleB-tNKT-liver-b Unknown   None    SampleB      NONE         2 narrow
7  SampleB-tNKT-liver-c Unknown   None    SampleB      NONE         3 narrow
8  SampleB-tNKT-liver-d Unknown   None    SampleB      NONE         4 narrow
9  SampleC-tNKT-liver-a Unknown   None    SampleC      NONE         1 narrow
10 SampleC-tNKT-liver-b Unknown   None    SampleC      NONE         2 narrow
11 SampleC-tNKT-liver-c Unknown   None    SampleC      NONE         3 narrow
12 SampleC-tNKT-liver-d Unknown   None    SampleC      NONE         4 narrow
   Intervals
1      28875
2      29934
3      29080
4      32218
5      29756
6      32381
7      29291
8      30393
9      30574
10     31420
11     32697
12     32395

data <- DiffBind::dba.count(data, summits = 250)
Re-centering peaks...
Error in heights * sapply(called, function(x) x) : non-conformable arrays

data <- DiffBind::dba.count(data, summits = T)
data

8 Samples, 29536 sites in matrix:

                   ID  Tissue Factor Condition Treatment Replicate Caller
1 SampleA-tNKT-liver-a Unknown   None    SampleA      NONE         1 counts
2 SampleA-tNKT-liver-b Unknown   None    SampleA      NONE         2 counts
3 SampleA-tNKT-liver-c Unknown   None    SampleA      NONE         3 counts
4 SampleA-tNKT-liver-d Unknown   None    SampleA      NONE         4 counts
5 SampleB-tNKT-liver-a Unknown   None    SampleB      NONE         1 counts
6 SampleB-tNKT-liver-b Unknown   None    SampleB      NONE         2 counts
7 SampleB-tNKT-liver-c Unknown   None    SampleB      NONE         3 counts
8 SampleB-tNKT-liver-d Unknown   None    SampleB      NONE         4 counts

  Intervals FRiP
1     29536 0.53
2     29536 0.49
3     29536 0.48
4     29536 0.46
5     29536 0.38
6     29536 0.49
7     29536 0.48
8     29536 0.50

I am unable to make it work with summits=250 and I need to be able to do that. This is ATACSeq data. 

Thanks,
Ashu

 

 

 

 

ADD COMMENTlink modified 17 days ago • written 17 days ago by Ashu10
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