 Dear bioc-sig-sequencing,

Regarding the "laneSubsample() in the chipseq package" suggestion.  Example usage for this from the chipseq manual shows

laneSubsample(lane1, lane2, fudge = 0.05)

with lane1 & lane2 parameters being of class "GenomeData".

As noted, after reading in the two files (ctcf, gfp), I would have AignedRead objects.  I assume I would need to convert each to a GenomeData object to use the 'laneSubsample' command?

I assume two GenomeData objects would be the output?  I would then need to convert the reduced size GenomeData object resulting from the initially larger GenomeData object, back to an AlignedRead object?  Then could proceed with the page 6 & 7 steps previously referenced to determine FDR cutoff.

Can someone indicate if this will work, and if so, indicate how to do it?  And if not, suggest how an FDR cutoff may be determined?



Thanks,
pterry@huskers.unl.edu
P. Terry

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