[BioC] DiffBind - Scores for peakset are all the same
António Domingues
amjdomingues at gmail.com
Sat Feb 9 17:32:31 CET 2013
Dear Gordon, Rory and Bioconductors,
I was using successfully Diff Bind last year, and I was picking up were
I left but things are not going smoothly. The loading of the samples
seem to be ok:
#############
library(DiffBind)
H3K4m3 = dba(sampleSheet="samplesheet_all.csv")
H3K4m3
# 8 Samples, 19885 sites in matrix (24260 total):
# ID Tissue Factor Condition Replicate Peak.caller Intervals
# 1 woJarid1 Hela H3K4me3 wo_Jarids 1 QuEST 14111
# 2 woJarid2 Hela H3K4me3 wo_Jarids 2 QuEST 13771
# 3 indJarid1 Hela H3K4me3 ind_Jarids 1 QuEST 14865
# 4 indJarid2 Hela H3K4me3 ind_Jarids 2 QuEST 13393
# 5 woJarid1 Hela H3K4me3 wo_Jarids 1 MACS 19144
# 6 woJarid2 Hela H3K4me3 wo_Jarids 2 MACS 20391
# 7 indJarid1 Hela H3K4me3 ind_Jarids 1 MACS 22899
# 8 indJarid2 Hela H3K4me3 ind_Jarids 2 MACS 24616
And the problem is in dba.count:
H3K4m3 = dba.count(H3K4m3)
# Warning messages:
# 1: Scores for peakset indJarid1 are all the same -- correlations set
to zero.
# 2: Scores for peakset indJarid2 are all the same -- correlations set
to zero.
# 3: Scores for peakset woJarid1 are all the same -- correlations set to
zero.
# 4: Scores for peakset woJarid2 are all the same -- correlations set to
zero.
I have no idea why this is happening. I wonder if there is something
that changed in the most recent version or I am missing something. Could
you please help and point me in the right direction? Maybe I am missing
something silly. The sample sheet is attached.
Cheers,
António
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] parallel grid grDevices datasets utils graphics stats
[8] methods base
other attached packages:
[1] ChIPpeakAnno_2.6.0 limma_3.14.4
[3] org.Hs.eg.db_2.8.0 GO.db_2.8.0
[5] RSQLite_0.11.2 DBI_0.2-5
[7] BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.26.1
[9] Biostrings_2.26.3 multtest_2.14.0
[11] biomaRt_2.14.0 VennDiagram_1.5.1
[13] DiffBind_1.4.1 GenomicFeatures_1.10.1
[15] GenomicRanges_1.10.5 IRanges_1.16.4
[17] data.table_1.8.6 stringr_0.6.2
[19] ggplot2_0.9.3 plyr_1.8
[21] AnnotationDbi_1.20.2 Biobase_2.18.0
[23] BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] MASS_7.3-23 RColorBrewer_1.0-5 RCurl_1.95-3 Rsamtools_1.10.2
[5] XML_3.95-0.1 amap_0.8-7 bitops_1.0-5 colorspace_1.2-1
[9] dichromat_2.0-0 digest_0.6.2 edgeR_2.4.0 gdata_2.12.0
[13] gplots_2.11.0 gtable_0.1.2 gtools_2.7.0 labeling_0.1
[17] munsell_0.4 proto_0.3-10 reshape2_1.2.2 rtracklayer_1.18.1
[21] scales_0.2.3 splines_2.15.2 stats4_2.15.2 survival_2.37-2
[25] tools_2.15.2 zlibbioc_1.4.0
>
--
---------------------------------------------------------------------
António Miguel de Jesus Domingues, PhD
Neugebauer group
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 Dresden
Germany
http://people.mpi-cbg.de/domingue/home.html
e-mail: domingue at mpi-cbg.de
tel. +49 351 210 2481
The Unbearable Lightness of Molecular Biology
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