[BioC] Questions about Disease Progression Analysis

[Sean Davis]

On Mon, May 19, 2008 at 5:00 AM, LiGang <luzifer.li at gmail.com> wrote:
> Dear all,
>
>
>
> I am using cDNA two-channel array to study gene profiling of 5 different
> stages of thyroid disease. Was there any Bioconductor package to perform
> such disease progression analysis?
>
>
>
> I have found packages such as
> "maSigPro<http://bioconductor.org/packages/2.2/bioc/html/maSigPro.html>
> "  "Mfuzz <http://bioconductor.org/packages/2.2/bioc/html/Mfuzz.html>" and"
> timecourse <http://bioconductor.org/packages/2.2/bioc/html/timecourse.html>"
> to perform Microarray Time Course Data analysis, can these methods be used
> to carry out disease progression data analysis?

Hi, LiGang.  There is a real temptation to think of disease stage as a
process that occurs in an ordered fashion.  That is, stage I disease
is just early enough that it has not progressed to stage II, etc.  I
think that there is plenty of evidence that this not always (or even
often) the case, so I would be hesitant to treat the stages of thyroid
disease as a disease progression.

As for time course analysis, it usually examines the behavior of genes
in the same sample(s) over time; you will likely not have the same
person who has multiple stages of thyroid disease, so I am not sure
that these methods will be applicable in your situation, anyway.

Do you have clinical followup data?  Other clinical covariates?  And
how many samples do you have in your dataset?  All of these are
important questions that can guide the hypotheses that you might want
to test.

Hope that helps.

Sean