scoring CNs
marco
I wonder how to score the reliability of the CNs found by aroma
affymetrix.
I saw a psot about p-values, but I did not really manage to get
anything out of it.
I have a lot of CNs produced by paired analysis. Mostly very short 2
loci CNs and I would like to understand how reliable those are.
(see previous thread "interpretation of results fot total CN
analysis")
This is my code
acc <- AllelicCrosstalkCalibration(cs)
csC <- process(acc, verbose=verbose)
plm <- AvgCnPlm(csC, mergeStrands=TRUE, combineAlleles=TRUE,
shift=+300)
fit(plm, verbose=verbose)
ces <- getChipEffectSet(plm)
fln <- FragmentLengthNormalization(ces)
cesN <- process(fln, verbose=verbose)
cesA <- extract(cesN, c(1,3,7,11))
cesB <- extract(cesN, c(2,4,8,13))
cbs <- CbsModel(cesA, cesB)
At this point, following thread "p-value in paired total copy number
analysis"
fitList <-
fit(cbs,array=1,chromosome=22, .retResults=TRUE,verbose=verbose)
fit <- fitList[[1]][[22]]
> class(fit)
[1] "DNAcopy"
This should be correct ??
from my understanding this returns a DNAcopy::segment() which seems
not to contain any information about the p-values.
from segment help:
"Value:
a data frame with six columns. Each row of the data frame
contains a segment for which there are six variables: the sample
id, the chromosome number, the map position of the start of the
segment, the map position of the end of the segment, the number
of
markers in the segment, and the average value in the segment."
So at this point I am a little bit lost. In the DNAcopy package does
not seem to be any way to get the p-values...
Thanks!
Cheers
Marco
Henrik Bengtsson
On Tue, Aug 12, 2008 at 7:16 AM, marco <mazu...@gmail.com> wrote:
>
> Dear List,
>
> I wonder how to score the reliability of the CNs found by aroma
> affymetrix.
>
> I saw a psot about p-values, but I did not really manage to get
> anything out of it.
I understand that you found the Apr 2, 2008 thread 'p-value in paired
total copy number analysis':
> I have a lot of CNs produced by paired analysis. Mostly very short 2
> loci CNs and I would like to understand how reliable those are.
> (see previous thread "interpretation of results fot total CN
> analysis")
Found it:
>
> This is my code
>
> acc <- AllelicCrosstalkCalibration(cs)
> csC <- process(acc, verbose=verbose)
> plm <- AvgCnPlm(csC, mergeStrands=TRUE, combineAlleles=TRUE,
> shift=+300)
> fit(plm, verbose=verbose)
> ces <- getChipEffectSet(plm)
> fln <- FragmentLengthNormalization(ces)
> cesN <- process(fln, verbose=verbose)
> cesA <- extract(cesN, c(1,3,7,11))
> cesB <- extract(cesN, c(2,4,8,13))
> cbs <- CbsModel(cesA, cesB)
>
> At this point, following thread "p-value in paired total copy number
> analysis"
>
> fitList <-
> fit(cbs,array=1,chromosome=22, .retResults=TRUE,verbose=verbose)
> fit <- fitList[[1]][[22]]
>> class(fit)
> [1] "DNAcopy"
>
> This should be correct ??
Yes, that is correct. You grab the CBS estimates from array 1 on
Chr22 and get a 'DNAcopy' object.
>
>
> from my understanding this returns a DNAcopy::segment() which seems
> not to contain any information about the p-values.
>
> from segment help:
>
> "Value:
>
> a data frame with six columns. Each row of the data frame
> contains a segment for which there are six variables: the sample
> id, the chromosome number, the map position of the start of the
> segment, the map position of the end of the segment, the number
> of
> markers in the segment, and the average value in the segment."
Correct, it doesn't.
>
>
> So at this point I am a little bit lost. In the DNAcopy package does
> not seem to be any way to get the p-values...
Look at the help index of the DNAcopy package. There is for instance:
"segments.p p-values for the change-points"
Please post further questions on this to the Bioconductor list - the
home of DNAcopy - since at this stage of you analysis this is no
longer an aroma.affymetrix-specific question.
Cheers
Henrik
>
> Thanks!
>
> Cheers
>
> Marco
>
>
>
>
>
>
> >
>