[BioC] Error in dispersionPlot using cummeRbund
guest at bioconductor.org
Sun Jan 5 19:07:35 CET 2014
I'm new to RNA-seq analysis. And I'm now trying to use R to visualize the Galaxy data. I'm using the cummeRbund to deal with the data from cuffdiff in Galaxy.
Here is the codes I've run:
> cuff= readCufflinks (dbFile = "output_database", geneFPKM = "gene_FPKM_tracking", geneDiff = "gene_differential_expression_testing", isoformFPKM = "transcript_FPKM_tracking",isoformDiff = "transcript_differential_expression_testing", TSSFPKM = "TSS_groups_FPKM_tracking", TSSDiff = "TSS_groups_differential_expression_testing", CDSFPKM = "CDS_FPKM_tracking", CDSExpDiff = "CDS_FPKM_differential_expression_testing", CDSDiff = "CDS_overloading_diffential_expression_testing", promoterFile = "promoters_differential_expression_testing", splicingFile = "splicing_differential_expression_testing", rebuild = T)
CuffSet instance with:
Error in `$<-.data.frame`(`*tmp*`, "SCALE_X", value = 1L) :
replacement has 1 rows, data has 0
In addition: Warning message:
In max(panels$ROW) : no non-missing arguments to max; returning -Inf
Does any one know why there's error? My cummeRbund is the latest version, R is 2.15.3, and cuffdiff v1.3.0.
I've tried to search the internet for solutions but apparently it's not a problem that people discussed much.
Also, the original files were generated from Galaxy, and the three CDS files were empty. Would that cause the problem? If so, how should I solve it? I used reference sequence as the fasta file, and the gtf annotation file from Ensembl.
Thank you very much in advance!!!
-- output of sessionInfo():
R version 2.15.3 (2013-03-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
 LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
 LC_TIME=English_United States.1252
attached base packages:
 splines grid stats graphics grDevices utils datasets methods base
other attached packages:
 edgeR_3.0.8 limma_3.14.4 affycoretools_1.30.0 KEGG.db_2.8.0
 GO.db_2.8.0 AnnotationDbi_1.20.7 WGCNA_1.34 Hmisc_3.13-0
 Formula_1.1-1 survival_2.37-2 lattice_0.20-13 cluster_1.14.3
 flashClust_1.01-2 dynamicTreeCut_1.60-1 plyr_1.8 affy_1.36.1
 Biobase_2.18.0 cummeRbund_2.0.0 Gviz_1.2.1 rtracklayer_1.18.2
 GenomicRanges_1.10.7 IRanges_1.16.6 fastcluster_1.1.13 reshape2_1.2.2
 ggplot2_0.9.3.1 RSQLite_0.11.4 DBI_0.2-7 BiocGenerics_0.4.0
loaded via a namespace (and not attached):
 affyio_1.26.0 annaffy_1.30.0 annotate_1.36.0 AnnotationForge_1.0.3
 biomaRt_2.14.0 Biostrings_2.26.3 biovizBase_1.6.2 bitops_1.0-5
 BSgenome_1.26.1 Category_2.24.0 codetools_0.2-8 colorspace_1.2-4
 dichromat_2.0-0 digest_0.6.4 doParallel_1.0.6 foreach_1.4.1
 gcrma_2.30.0 gdata_2.13.2 genefilter_1.40.0 GenomicFeatures_1.10.2
 GOstats_2.24.0 gplots_2.11.0 graph_1.36.2 GSEABase_1.20.2
 gtable_0.1.2 gtools_2.7.0 impute_1.32.0 iterators_1.0.6
 labeling_0.2 MASS_7.3-23 matrixStats_0.8.12 munsell_0.4.2
 parallel_2.15.3 preprocessCore_1.20.0 proto_0.3-10 R.methodsS3_1.5.2
 RBGL_1.34.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape_0.8.4
 Rsamtools_1.10.2 scales_0.2.3 stats4_2.15.3 stringr_0.6.2
 tools_2.15.3 XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.4.0
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