[BioC] maSigPro and "vars" argument

[Mª José Nueda]

Dear Andrea,

1) Your experimental design is correct.
2) Your explanation about the 2 groups you have when vars="groups" is also 
correct. Normally the first group is a reference (the control group) and 
maSigPro looks for genes that have differences between other treatments and 
the control. If you want to find genes with changes in time for the second 
group you can make 2 things: -Selecting group2 as the reference (first 
group) or, as you say, spliting the data in 2 groups. But this last option 
doesn't give you genes with differences  between groups.
3) Using vars="each" you get a many lists as variables you have in the 
model. The meaning "biologically speaking" depends on the study. This is an 
option that allows look for specific questions (differents to "all" or 
"groups") that a user can be interested in.  For instance,  if you are 
looking for all the genes with linear changes but not quadratic changes or 
whatever. You can manage these lists of genes to get the question you 
desire.

 If you don't understand my answer, please contact me again. Thank you for 
using maSigPro.

María J. Nueda.

--------------------------------------------------
From: <andrea.grilli at ior.it>
Sent: Thursday, September 08, 2011 5:41 PM
To: <bioconductor at r-project.org>
Subject: [BioC] maSigPro and "vars" argument

> 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
>
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