[BioC] Questions about Disease Progression Analysis

[LiGang]

Sean Davis <sdavis2 at ...> writes:

> 
> On Mon, May 19, 2008 at 5:00 AM, LiGang <luzifer.li at ...> 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
> 
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> 

Dear Sean,

Thanks for your reply!

In fact, there are no clinical parameters except the qualitative stage 
information.

Experiment details are listed below:

Chip	Stage	sample            
================================  
Chip_1 	Stage 1	mouse_1_thyroid   
Chip_2 	Stage 1	mouse_2_thyroid   
Chip_3 	Stage 1	mouse_3_thyroid   
Chip_4 	Stage 1	mouse_4_thyroid   
----------------------------------------------------   
Chip_5 	Stage 2	mouse_5_thyroid   
Chip_6 	Stage 2	mouse_6_thyroid   
Chip_7 	Stage 2	mouse_7_thyroid   
Chip_8 	Stage 2	mouse_8_thyroid   
----------------------------------------------------   
Chip_9 	Stage 3	mouse_9_thyroid   
Chip_10	Stage 3	mouse_10_thyroid  
Chip_11	Stage 3	mouse_11_thyroid  
Chip_12	Stage 3	mouse_12_thyroid  
----------------------------------------------------  
Chip_13	Stage 4	mouse_13_thyroid  
Chip_14	Stage 4	mouse_14_thyroid  
Chip_15	Stage 4	mouse_15_thyroid  
Chip_16	Stage 4	mouse_16_thyroid  
----------------------------------------------------  
Chip_17	Stage 5	mouse_17_thyroid  
Chip_18	Stage 5	mouse_18_thyroid  
Chip_19	Stage 5	mouse_19_thyroid  
Chip_20	Stage 5	mouse_20_thyroid  
================================  

and all 20 hybridizations use the same common reference sample (pooled samples 
of normal tissues from the above 20 mice).  

My aim is to identify genes that are up-regulated or down-regulated as thyroid 
disease progresses and even whether there exist genes which have a specific 
trend.

Is it rational to:

1)	perform pairwise comparisons
2)	Select the Union set of all genes whose expression level changed       
between any arbitrary pairwise comparisons.
3)	Do cluster analysis to see the trends.

---
LiGang