rhv-report-plots.pdf   13 gene classifier and plots for Rhino study
rsv-report-plots.pdf   13 gene classifier and plots for RSV study
rsvnon-report-plots.pdf plots from RSV immunoassay results
rsv-meta-plots.pdf      plots from RSV metabolomics results
flu-report-plots.pdf   13 gene classifier and plots for Influenze study


Classifier description:
The classifier uses the following 13 genes:
secreted factors: CXCL10, OAS2, CCL2, CCL8, IL1B, IL1RN
internal factors: CASP7
surface factors: CCR1, TAP1, TAP2
viral specific factors: CASP5
HRV specific factors: TNFAIP6, TNFSF10

We use significant over-expression  of a gene at any time point
as an indicator.  "Significant over-expression" here means that 
the expression level is significantly above the average levels at 
T-12 and T0 (averaged over all individuals).
Most of the genes in the list above are known to show a 
"Middle Transient", "Middle Stationary", 
"Early Transient", or "Early Stationary" response to an infection.

The classifier works as follows:  given some data points for a 
particular subject, the classifier counts the number of data points
wherein one of the above genes is significantly over-expressed.  If 
this score (number of over-expressions) is above a certain threshold, 
then the subject is classified as having "either sero-converted or shed".
If not, then the subject is left unclassified.

Table of results for Rhino infection (RSV and Flu classification in plots file)
----------------------------------
No subject is ever wrongly classified, but several may be left unclassified
  in our approach. 
Time points used  :  Number of individual not classified 
--------------------------------------------------------
  0--96	          :  9
  0--48            :  10
  0--30            :  15
  0--24		  :  16
  0--12 		  :  17
  0--8		  :  18

We note that the 9 subjects that are unclassified (using all time points 
from T0 to T96) are all "asymptomatic" with the exception of subject 9 
who is mildly symptomatic.