[Bioc-devel] Genomics analysis results class

[Luigi Marchionni]

Dear developers,
my name is Luigi Marchionni, I am Instructor in Oncology at Johns  
Hopkins.
I have ongoing research on various biological problems and I make use  
of GSEA like methods for which I wrote my own package.
I'd like to upload that in Bioconductor and for this reason I am  
updating my code to reuse as much as possible already implemented S4  
classes.

For the gene sets I am using GSEABase classes, however I did not find  
an existing class for results from genomics analyses.
I thought in the first place to extend the MultiSet class from  
Biobase, but this does not seem to be completely appropriate (I have  
results from different platforms and technologies, i.e. microarray and  
SAGE).

Right now I use a list of data.frames, each one storing the features  
identifiers and the ranking statistics from the genomics analyses  
(additional information could be obviously added in additional slots).  
See the object ex.Stats below as an example:

 > class(ex.Stats)
[1] "list"
 > str(ex.Stats)
List of 2
  $ ex.hgu133a :'data.frame':	100 obs. of  6 variables:
   ..$ ID       : chr [1:100] "200763_s_at" "200062_s_at"  
"208834_x_at" "214631_at" ...
   ..$ logFC    : num [1:100] -8.09 -6.71 -5.92 5.97 5.82 ...
   ..$ t        : num [1:100] -43.8 -31 -30.5 28.8 27.3 ...
   ..$ P.Value  : num [1:100] 1.89e-96 2.85e-73 3.25e-72 1.49e-68  
3.18e-65 ...
   ..$ adj.P.Val: num [1:100] 1.27e-92 9.57e-70 7.26e-69 2.50e-65  
4.26e-62 ...
   ..$ B        : num [1:100] 204 154 152 144 136 ...
  $ ex.hgu95av2:'data.frame':	100 obs. of  6 variables:
   ..$ ID       : chr [1:100] "31957_r_at" "35777_at" "32412_at"  
"32539_at" ...
   ..$ logFC    : num [1:100] -7.76 -6.93 -5.66 5.72 5.68 ...
   ..$ t        : num [1:100] -41 -31.3 -28.5 27 26 ...
   ..$ P.Value  : num [1:100] 7.05e-92 8.77e-74 8.49e-68 2.16e-64  
3.29e-62 ...
   ..$ adj.P.Val: num [1:100] 4.73e-88 2.94e-70 1.90e-64 3.63e-61  
4.41e-59 ...
   ..$ B        : num [1:100] 194 155 142 134 130 ...

This works just fine, however, I do not want to reinvent the wheel...
I was discussing with Rafa and he suggested that before I go any  
further with coding I inquire with you guys if anything like this  
already exists.
He said that Vincent Carey might have already something for that.
Is that true? Do you have any suggestion?

I thank all of you in advance,

Luigi Marchionni

--
Ulisse: "Considerate la vostra semenza:
fatti non foste a viver come bruti,
ma per seguir virtute e canoscenza".
(Dante, Divina Commedia, Canto XXVI)
--
      G-C
     T---A    Luigi Marchionni, M.D., Ph.D.
    C----G    The Sidney Kimmel Comprehensive Cancer Center
G-------C    Johns Hopkins University -  School of Medicine
   A------T     1550 Orleans St., CRB2, Rm 554
     C----G    Baltimore, MD, 21231, USA
     G--C    Tel: (001) 410-502-8179
      C-G    Fax: (001) 410-502-5742
     T---A    e-mail: marchion at jhmi.edu
    G-----C    URL: http://astor.som.jhmi.edu/~marchion/
   A-------T