Hi Gordon,

I thougth that might be the problem but the Vignette (20 March 2012) states
that SAM could be used "Additionally, file containing mapped sequencing
reads (BAM/SAM/BED) can be associated with each peakset". Not a problem
though, converting to BAM is easy enough.


P.S. "chr, start, end, score" isn't technically a legal bed file.  You'd
> need "chr, start, end, NAME, score" for it to be a bed file.  Though
> DiffBind may read them anyway (I didn't write that part...).


Yes of course, I've completely forgot that.

Cheers.
António

On 14 September 2012 12:28, Gordon Brown <Gordon.Brown@cancer.org.uk> wrote:

> Hi, António,
>
> DiffBind doesn't read SAM format, only BAM and (gzipped or uncompressed)
> BED.  Try converting your SAM files to BAM.
>
> Cheers,
>
>  - Gord
>
> P.S. "chr, start, end, score" isn't technically a legal bed file.  You'd
> need "chr, start, end, NAME, score" for it to be a bed file.  Though
> DiffBind may read them anyway (I didn't write that part...).
>
>
>
> On 2012-09-14 10:58, "António Miguel de Jesus Domingues"
> <amjdomingues@gmail.com> wrote:
>
> >Hi again,
> >
> >I am trying DiffBind and loaded my data that looks like this:
> >
> >H3K4m3
> >4 Samples, 13203 sites in matrix (13792 total):
> >         ID Tissue  Factor  Condition Peak.caller Replicate Intervals
> >1  wt1   Hela H3K4me3  control1         raw         1     14111
> >2  wt2   Hela H3K4me3  control2         raw         2     13771
> >3 treat1   Hela H3K4me3 condition1         raw         1     14865
> >4 treat2   Hela H3K4me3 condition2         raw         2     13393
> >
> >But I ran into problems trying to calculate the affinity scores with
> >dba.count:
> >
> >H3K4m3 = dba.count(H3K4m3)
> >Error in cond$counts : $ operator is invalid for atomic vectors
> >In addition: Warning message:
> >In mclapply(arglist, fn, ..., mc.preschedule = FALSE) :
> >  6 function calls resulted in an error
> >
> >The peaks are in bed files (chr, start, end, score) and the reads are in
> >SAM format.
> >
> >Can anyone help me with this?
> >
> >Cheers.
> >António
> >
> >> sessionInfo()
> >R version 2.14.1 (2011-12-22)
> >Platform: x86_64-pc-linux-gnu (64-bit)
> >
> >locale:
> >[1] C
> >
> >attached base packages:
> >[1] parallel  stats     graphics  grDevices utils     datasets  methods
> >[8] base
> >
> >other attached packages:
> >[1] DiffBind_1.0.9 Biobase_2.14.0
> >
> >loaded via a namespace (and not attached):
> >[1] IRanges_1.12.6     RColorBrewer_1.0-5 amap_0.8-7
> >edgeR_2.4.6
> >[5] gdata_2.11.0       gplots_2.11.0      gtools_2.7.0
> >limma_3.10.3
> >[9] zlibbioc_1.0.1
> >>
> >
> >On 13 September 2012 18:06, António Miguel de Jesus Domingues <
> >amjdomingues@gmail.com> wrote:
> >
> >> Hi all,
> >>
> >> I am trying to use DiffBind to compare peaks called in control vs
> >> condition. I have 2 replicates for each and I've also called peaks
> >>using 2
> >> different peak callers (to wi, MACS and QuEST). I've also prepared a
> >>sample
> >> data sheet that looks like this:
> >> SampleID   Tissue   Factor   Condition   Replicate  Peak.caller
> >>bamReads
> >> bamControl   Peaks
> >> control         Hela      TF              wt              1
> >> MACS          path             path                path
> >> control         Hela      TF              wt              1
> >> QuEST         path             path                path
> >> control2       Hela      TF            wt              2
> >> MACS          path             path                path
> >> control 2      Hela      TF            wt              2
> >> QuEST         path             path                path
> >> (and the same for the conditions)
> >>
> >> My plan was to load all the data and then using diffbind selecte a set
> >>of
> >> common peaks for the peak callers before proceeding with the analysis.
> >> However, when I load the data (data =
> >>dba(sampleSheet="samplesheet.csv"))
> >> the peaks for each caller are not recognized as a different variable.
> >>How
> >> I can do that and is this silly?
> >>
> >> I could also derive a set of common peaks independently but it would be
> >> neat to do it all with the same package and that seems to be possible
> >>but I
> >> could not find how to do it in the documentation.
> >>
> >> Thanks,
> >> António
> >>
> >>
> >> --
> >> --
> >> António Miguel de Jesus Domingues, PhD
> >> Neugebauer group
> >> Max Planck Institute of Molecular Cell Biology and Genetics, Dresden
> >> Pfotenhauerstrasse 108
> >> 01307 Dresden
> >> Germany
> >>
> >> e-mail: domingue@mpi-cbg.de
> >> tel. +49 351 210 2481
> >> The Unbearable Lightness of Molecular Biology
> >>
> >
> >
> >
> >--
> >--
> >António Miguel de Jesus Domingues, PhD
> >Neugebauer group
> >Max Planck Institute of Molecular Cell Biology and Genetics, Dresden
> >Pfotenhauerstrasse 108
> >01307 Dresden
> >Germany
> >
> >e-mail: domingue@mpi-cbg.de
> >tel. +49 351 210 2481
> >The Unbearable Lightness of Molecular Biology
> >
> >       [[alternative HTML version deleted]]
> >
> >
>
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-- 
-- 
António Miguel de Jesus Domingues, PhD
Neugebauer group
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden
Pfotenhauerstrasse 108
01307 Dresden
Germany

e-mail: domingue@mpi-cbg.de
tel. +49 351 210 2481
The Unbearable Lightness of Molecular Biology

	[[alternative HTML version deleted]]

