DiffBind

headers António Domingues | 9 Feb 2013 17:32

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@...
tel. +49 351 210 2481
The Unbearable Lightness of Molecular Biology

DiffBind - Scores for peakset are all the same