User: SeshanV@mskcc.org

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Posts by SeshanV@mskcc.org

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Comment: C: DNACopy Question what is passed to the maploc argument.
... As you have figured, technically any numeric value that preserves the probe ordering along a chromosome is valid. You only need the actual value to map it back to the genome. Since you don't observe anything between the end of a probe and the start of the next probe, you can only say that the break ...
written 3.3 years ago by SeshanV@mskcc.org40
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Comment: C: DNACopy Question what is passed to the maploc argument.
... Hi Nikolas, Here is what the help for CNA says: maploc: the locations of marker on the genome. Vector of length same as the number of rows of genomdat. This has to be numeric. That is, it is the genomic position at which the copy number information is being measured. In the link t ...
written 3.3 years ago by SeshanV@mskcc.org40
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Answer: A: Error in sort(abs(diff(genomdat)))[1:n.keep]
... The error may be the result of your call rather than either of the packages. Note that your call has "sdundo=c(0,0), alpha=c(0.5,0.1)" whereas the defaults from the manual is "sdundo=c(1,2), alpha=c(0.05,0.01)." Venkat -----Original Message----- From: wwwrun@mamba.fhcrc.org [mailto:wwwrun@mamba.f ...
written 4.5 years ago by SeshanV@mskcc.org40
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Answer: A: DNAcopy segment() Infinite Loop
... There is something weird in your data set. Of the 154005 values there are 137109 unique ones. Oddly there are 16335 that have the same value. > table(table(cn$Fold.Change)) 1 2 3 4 5 9 16335 135779 883 31 3 1 1 1 Those 16335 repeated va ...
written 6.4 years ago by SeshanV@mskcc.org40

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