hello Xiaowei,
    If I have understood correctly, from a training data set (where case &
control are defined) you have identified a set of 'classifier' genes. Using
these then you would like to check case vs. control separation in your test
data set.
 Seems fine and absolutely do-able. Only concern would be whether your
training and test data set are of similar type/ platform or
not. Heterogeneous experimental platform might bring in noise.


best,

amit m

Graduate student
IGIB, Delhi

On Thu, Feb 24, 2011 at 11:39 AM, Xiaowei Guan <xxg39@case.edu> wrote:

> Dear Sir or Madam,
>
> I have a question about performing PCA method on the gene expression data.
> If I have a training dataset and I identified a smaller set of genes as
> biomarkers to predict case and control status.... What if I only select
> those genes from the validation dataset and make some prediction of the
> case-control status  with the loadings of each gene in that smaller set of
> biomarkers?
>
> Thanks very much.
>
> best,
> Xiaowei
>
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