[BioC] maSigPro and "vars" argument

[andrea.grilli at ior.it]

Hi to all,
I'm analyzing time series experiment with maSigPro package as first  
time, and I get problems to understand if experimental design is  
correct or not, in particular I'm doubtful with "vars" argument.

Data comes from Affymetrix gene chip from 2 different cell lines, 4  
time points, 2 replicates at each time. I normalized with RMA, and  
filtered out low expressed/low changing genes, getting from initial  
54k probes about 12k probes.

I'm interested in genes varying (i)in either cell lines between the  
different time points (ii) between the two cell lines across time.

I did the analysis with vars argument as "groups", getting these comparisons:
> (ts.analysis$sig.genes$)
ts.analysis$sig.genes$Group1        ts.analysis$sig.genes$Group2vsGroup1

So, If I well understood, I have 2 gene sets of significant genes, the  
first with those changing across time in Group1 cells, the second with  
those changing in Group2 vs Group1 cells across time.

My questions: how can I also get significant genes for Group2?? Should  
I split the experiment in two parts and performing separately?
Last question: using vars = "each", what I exactly get? I mean  
biologically speaking...



This is my design matrix:
           Time Replicates Group1 Group2
wt22_g21    21          1            1    0
wt22_g7      7          2            1    0
wt36_g21    21          1            1    0
wt36_g7      7          2            1    0
Saos1_g21   21          5            0    1
Saos2_g21   21          5            0    1
Saos1_g7     7          6            0    1
Saos2_g7     7          6            0    1
wt22_g0      0          3            1    0
wt22_g14    14          4            1    0
wt36_g0      0          3            1    0
wt36_g14    14          4            1    0
Saos1_g0     0          7            0    1
Saos2_g0     0          7            0    1
Saos1_g14   14          8            0    1
Saos2_g14   14          8            0    1

This is the command line:
> ts.analysis <- maSigPro (Data, parameters2, min.obs=4, rsq=0.7,  
> step.method="backward", pdf = TRUE, main = "./results.pdf", alfa =  
> 0.05, degree = 2, k = 9, vars = "groups")

I checked in Bioconductor documentation, but things remain confused to me.
Any clarification is really appreciated,
Thanks,
Andrea


Dr. Andrea Grilli
andrea.grilli at ior.it
phone 051/63.66.756

Laboratory of Experimental Oncology
Rizzoli Orthopaedic Institute
Codivilla Putti Research Center
via di Barbiano 1/10
40136 - Bologna - Italy