Rory Stark | 9 Feb 19:09 2013
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Re: DiffBind - Scores for peakset are all the same

Hi António-

I've seen something like this once before.

Could you share your DBA object H3K4m3 (after the call to dba.count) with me, either as an FTP or Dropbox, so I
can troubleshoot this?

Cheers-

Rory

________________________________
From: António Domingues [amjdomingues@...]
Sent: 09 February 2013 16:32
To: Gordon Brown; bioconductor@...; Rory.Stark@...
Subject: DiffBind - Scores for peakset are all the same

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
>

--
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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@...<mailto:domingue@...>
tel. +49 351 210 2481
The Unbearable Lightness of Molecular Biology

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