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Question: DiffBind dba.plotHeatmap Error in hclustfun(distfun(x))
0
gravatar for Gary
11 weeks ago by
Gary0
Gary0 wrote:

Hi

When I run dba.plotHeatmap command below, there is an error message:

> dba.plotHeatmap(h3k27ac, attributes = DBA_ID, ColAttributes = c(DBA_CONDITION, DBA_TISSUE), colSideCols = c("deepskyblue", "deeppink"), correlations = FALSE, colScheme = "Blues", scale = "row", maxSites = 1000, margin = 13)

Error in hclustfun(distfun(x)) :

NA/NaN/Inf in foreign function call (arg 11)

The below are all commands I performed for reference.

Best & many thanks,

Gary

> setwd("/Volumes/NCHU/20170811_Tang_MandarinDuck/20170815_analysis/diffbind")
> require("DiffBind")
Loading required package: DiffBind
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

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

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    colMeans, colSums, expand.grid, rowMeans, rowSums

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")'.


> h3k27ac <- dba(sampleSheet = "h3k27ac.csv")
MSailH3K27ac_C153 Sail H3K27ac Male C153 1 narrow
MSailH3K27ac_C156 Sail H3K27ac Male C156 2 narrow
MFlightH3K27ac_C159 Flight H3K27ac Male C159 1 narrow
MFlightH3K27ac_C165 Flight H3K27ac Male C165 2 narrow
FSailH3K27ac_C168 Sail H3K27ac Female C168 1 narrow
FSailH3K27ac_C171 Sail H3K27ac Female C171 2 narrow
FFlightH3K27ac_C177 Flight H3K27ac Female C177 1 narrow
FFlightH3K27ac_C180 Flight H3K27ac Female C180 2 narrow
> h3k27ac
8 Samples, 13047 sites in matrix (19937 total):
                   ID Tissue  Factor Condition Treatment Replicate Caller Intervals
1   MSailH3K27ac_C153   Sail H3K27ac      Male      C153         1 narrow     10373
2   MSailH3K27ac_C156   Sail H3K27ac      Male      C156         2 narrow      9158
3 MFlightH3K27ac_C159 Flight H3K27ac      Male      C159         1 narrow      9622
4 MFlightH3K27ac_C165 Flight H3K27ac      Male      C165         2 narrow      9059
5   FSailH3K27ac_C168   Sail H3K27ac    Female      C168         1 narrow     10853
6   FSailH3K27ac_C171   Sail H3K27ac    Female      C171         2 narrow     15717
7 FFlightH3K27ac_C177 Flight H3K27ac    Female      C177         1 narrow     12572
8 FFlightH3K27ac_C180 Flight H3K27ac    Female      C180         2 narrow     11963
> plot(h3k27ac)
> dba.plotHeatmap(h3k27ac, attributes = DBA_ID, ColAttributes = c(DBA_CONDITION, DBA_TISSUE), colSideCols = c("mediumpurple1", "palegreen2"), correlations = FALSE, colScheme = "Blues", scale="row", maxSites = 1000)
> dba.plotPCA(h3k27ac, attributes = DBA_CONDITION, dotSize = 3, cor = TRUE, vColors = c("deepskyblue", "deeppink"))
> dba.plotPCA(h3k27ac, attributes = DBA_TISSUE, dotSize = 3, cor = TRUE, vColors = c("goldenrod1", "mediumblue"))
> savefile <- dba.save(h3k27ac, file = "h3k27ac_peaks")
> h3k27ac <- dba.load(file = "h3k27ac_peaks")
> h3k27ac <- dba.count(h3k27ac, minOverlap = 2, score = DBA_SCORE_TMM_MINUS_EFFECTIVE_CPM, fragmentSize = 0, bRemoveDuplicates = TRUE, bScaleControl = TRUE, mapQCth = 10, bCorPlot = TRUE, bUseSummarizeOverlaps = TRUE, bParallel = TRUE)
> dba.plotHeatmap(h3k27ac, attributes = DBA_ID, ColAttributes = c(DBA_CONDITION, DBA_TISSUE), colSideCols = c("deepskyblue", "deeppink"), margin = 13)
> dba.plotHeatmap(h3k27ac, attributes = DBA_ID, ColAttributes = c(DBA_CONDITION, DBA_TISSUE), colSideCols = c("deepskyblue", "deeppink"), correlations = FALSE, colScheme = "Blues", scale = "row", maxSites = 1000, margin = 13)
Error in hclustfun(distfun(x)) : 
  NA/NaN/Inf in foreign function call (arg 11)

ADD COMMENTlink modified 9 weeks ago by Rory Stark2.1k • written 11 weeks ago by Gary0
1
gravatar for Rory Stark
11 weeks ago by
Rory Stark2.1k
CRUK, Cambridge, UK
Rory Stark2.1k wrote:

Hi Gary-

If you could email me the DiffBind object (h3k27ac) I can see if I can reproduce this and resolve the issue.

Regards-

Rory

ADD COMMENTlink written 11 weeks ago by Rory Stark2.1k
0
gravatar for Rory Stark
9 weeks ago by
Rory Stark2.1k
CRUK, Cambridge, UK
Rory Stark2.1k wrote:

This turned out to be a bug in DiffBind when there are rows in the binding matrix will all zero values. I am checking in a fix for the next release. 

There is a work-around you can use in the meantime, which is to set the sortFun parameter to sd:

> dba.plotHeatmap(h3k27ac, attributes = DBA_ID, 
                  ColAttributes = c(DBA_CONDITION, DBA_TISSUE), 
                  colSideCols = c("deepskyblue", "deeppink"), 
                  correlations = FALSE, colScheme = "Blues", 
                  scale = "row", maxSites = 1000, margin = 13, 
                  sortFun=sd)

I will be making this the default in the next release.

Cheers-

Rory

ADD COMMENTlink written 9 weeks ago by Rory Stark2.1k
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