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)
>
