On Wed, Nov 3, 2010 at 3:37 AM, rasanpreet kaur suri <
rasanpreet.kaur@gmail.com> wrote:

> Dear Sean,
>
> Thanks for your reply. Probably i should not ask this question across
> bioc as i dont have any other source to ask, i'm putting this question
> across to you. I'm sorry for not explaining the problem in my previous
> email, After seeing your email i figured that i already have TRUE
> values.
>
> We have conducted the following experiment:
>
> We have performed DSBR assay and acquired  SSF(DNA repair) values and
> genotype information for Placebo (control) and drug sample. We have a
> total of 116 samples of which 58 are placebo and 58 are drug samples.
> The objective of doing ROC is to get an optimal threshold value to
> find if there is any association between the genotype information and
> SSF (trait) value for Drug sample and placebo separately. Having that
> as an objective, using "placebo" and "drug" as classifiers, we will
> end up with one cut-off value. Using this cut-off I would like to
> perform chi-sqaure test for drug SSF values and placebo SSF values to
> get the genotypes associated with more DNA damage (i.e SSF>cut-off
> will imply more damage) and less damage(i.e SSF<cut-off will imply DNA
> repair).
>
>
If you are looking for genotype differences, then test that directly using a
hypothesis test.  In this case, it sounds like you have a two-factor setup,
treatment and genotype, with genotype being the factor of interest.  Why not
test for differences in SSF values between the genotypes?  A simple place to
start is with plotting the data using something like ggplot2 or lattice to
allow you to see if there are observable differences.


> If that is the case, will that make sense to have "Placebo" and "drug"
> as classifiers in ROC?
>
>
I don't think so.  I don't see how ROC curves will be useful given what you
describe above as your question.  I could be mistaken, though.

Sean


> Thanking you in anticipation,
>
> Regards,
> Rasanpreet Kaur
>
> On Sat, Oct 30, 2010 at 6:26 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:
> >
> >
> > On Sat, Oct 30, 2010 at 12:35 AM, rasanpreet kaur suri
> > <rasanpreet.kaur@gmail.com> wrote:
> >>
> >> Hello friends,
> >> I want to perform ROC analysis on a list of Strand scission factor
> values.
> >> eg:
> >> SSF_value
> >> 0.123
> >> 0.345
> >> 0.235
> >> 0.546
> >> ..
> >>
> >> I have no binary trait to perform the analysis. Could you please let me
> >> know
> >> how proper it is to simulate values or classifiers to get a threshold
> >> value
> >> and which function i can use to simulate the classifiers. I will be
> >> thankful
> >> for any knid of advice.
> >>
> >
> > Hi, Rasanpreet.  You need to know the "true" values for a classifier so
> that
> > you can determine sensitivity and specificity of the test.  Without those
> > values, I'm not sure how how ROC curves would be applied.
> > Sean
> >
> >>
> >> Thanking you in anticipation.
> >>
> >> Regards,
> >> Rasanpreet Kaur
> >>
> >>        [[alternative HTML version deleted]]
> >>
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> >
> >
>
>
>
> --
> Rasanpreet Kaur
>
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