On Fri, Jun 11, 2010 at 12:08 PM, [email protected] < [email protected]> 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, > [email protected] > P. Terry > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
