On Fri, Jun 11, 2010 at 12:08 PM, pterry@huskers.unl.edu <
pterry@huskers.unl.edu> wrote:

>  Dear bioc-sig-sequencing,
>
> I would like to determine a cutoff/threshold for a chipseq experiment for
> defining a FDR (BasicChipSeq.pdf, A ChIP-Seq Data Analysis, page 6 & 7, EX
> 2,
> http://www.bioconductor.org/workshops/2009/SeattleNov09/ChIP-seq/BasicChipSeq.pdf
> ).
>
> After reading in the two files (ctcf, gfp), have AignedRead objects.
>  Before running code on page 6 & 7 for ctcf and gfp data (to find
> distribution of depths compared to the null distributions), would like to
> account for (equalize) any difference between the number of reads between
> ctcf, gfp data sets.  Is there a recommended way to do this?
>
>
See laneSubsample() in the chipseq package for one approach.


> For example, perhaps
>
> 1. One could use the R function 'sample' somehow on the AlignedRead object
> (ctcf or gfp) with more reads to produce a subset of reads equal to the
> number in the smaller file?  Repeat say 3 times to control for sampling
> variation when determining the cutoff described above?
>
>
> 2. Or perhaps sort of similar to slide 25 in workshop (CoverageEDA.pdf,
> http://bioconductor.org/packages/courses/seattle-01-2009/day3/CoverageEDA.pdf),
> find/create an R function that could multiply an Rle object, here ctcf or
> gfp (the depth value for each nucleotide) by the fraction representing the
> relationship between the number of reads in the two AlignedRead objects.
>  This followed by applying 'round' function as done in slide 25 to give
> integer values for the depth values in the Rle object?
> (I note the '2009' in this URL should be '2010'?)
>
> Can someone comment?
>
>
> Thanks,
> pterry@huskers.unl.edu
> P. Terry
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>

	[[alternative HTML version deleted]]

