[BioC] ROC query

rasanpreet kaur suri rasanpreet.kaur at gmail.com
Wed Nov 3 08:37:17 CET 2010

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

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

If that is the case, will that make sense to have "Placebo" and "drug"
as classifiers in ROC?

Thanking you in anticipation,

Rasanpreet Kaur

On Sat, Oct 30, 2010 at 6:26 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Sat, Oct 30, 2010 at 12:35 AM, rasanpreet kaur suri
> <rasanpreet.kaur at 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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