Hello list
I have tried to run DBChIP in order to compare two IP libraries with no
replicates (yes I know, very bad design but this is what I have)
While trying to solve the errors I got, I think I have found few bugs

1. In cases where one sample has peaks on a chromosome which is missing
from the other sample I got the error below:

>dat <- load.data(chip.data.list=chip.data.list, conds=conds,
consensus.site=consensus.site, input.data.list=input.data.list, data.type="
AlignedRead",chr.exclusion = extracted[,1],frag.len=100)






*reading data...donecomputing normalization factor between ChIP and control
samples....................Error in hist.default(x[[chr]][["+"]], breaks =
bk.f, plot = FALSE) :   'x' must be numericIn addition: Warning messages:1:
In max(y[[x]][["+"]]) : no non-missing arguments to max; returning -Inf2:
In max(y[[x]][["+"]]) : no non-missing arguments to max; returning -Inf*

In my case I had a single peak on one of the "undefined" chromosomes in
sample1, and no peaks on that chromosome for sample 2.
After removing this peak from the list, the command run with no problems.

2. Another error I got was when trying to run the following command
>dat <- test.diff.binding(dat)


*Error in binom.test(x[1], n = x[2], p = x[3], alternative = "two.sided") :
'n' must be a positive integer >= 'x'*

I looked for the problematic rows in the "data" object, and found 25 like
these:

chr10_111494827 0     0  NaN
chr10_128493538 0     0  NaN
chr11_100503198 0     0  NaN

After removing these 25 sites from the original peak list, the command run
successfully.
Do you have any idea why I got here "0" values although in the original
list there are reads mapped to these peaks?

Thanks
Mali


> sessionInfo()
\R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=C                LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] ShortRead_1.20.0     Rsamtools_1.14.2     Biostrings_2.30.1
 [4] GenomicRanges_1.14.4 XVector_0.2.0        IRanges_1.20.6
 [7] DBChIP_1.6.0         DESeq_1.14.0         lattice_0.20-15
[10] locfit_1.5-9.1       Biobase_2.22.0       BiocGenerics_0.8.0
[13] edgeR_3.4.2          limma_3.16.7

loaded via a namespace (and not attached):
 [1] annotate_1.40.0      AnnotationDbi_1.24.0 bitops_1.0-5
 [4] DBI_0.2-7            genefilter_1.44.0    geneplotter_1.40.0
 [7] grid_3.0.1           hwriter_1.3          latticeExtra_0.6-26
[10] RColorBrewer_1.0-5   RSQLite_0.11.4       splines_3.0.1
[13] stats4_3.0.1         survival_2.37-4      tools_3.0.1
[16] XML_3.98-1.1         xtable_1.7-1         zlibbioc_1.6.0

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