[BioC] A couple VSN related questions

[Leo J. LEE]

Dear all,

I am new to Bioconductor and R (having the latest version, Bioconductor 2.1
and R 2.6.1, installed) so please bear with me if I ask something
naive/stupid.  Anyway, the most important reason why I come to Bioconductor
is to use the vsn package, and after trying it a bit, I have the following
questions:

1. It is clear from the documentation (and a previous email from Wolfgang)
that the real computation of vsn2 is written in C.  Is it possible for me to
access the C source code (and compile and run it myself)?  If yes, this will
be truly great since I have to do other computational analysis outside of R
anyway.

2. I am trying to follow the computation performed by VSN as documented in
the "Introduction to VSN" vignette.  Loading the kidney dataset, I have the
following data before and after VSN:
> exprs(kidney)[1:10,]
     channels
spots  green    red
   1  815.32 937.02
   2  671.66 765.03
   3  713.93 713.59
   4  703.97 656.70
   5  493.59 472.10
   6  477.92 453.13
   7  346.55 385.47
   8  377.34 421.86
   9  132.80 121.77
   10 148.65 130.41
> fit = vsn2(kidney)
vsn: 8704 x 2 matrix (1 stratum). 100% done.
> fit at hx[1:10,]
     channels
spots    green      red
   1  9.711781 9.870624
   2  9.453765 9.597638
   3  9.533994 9.506128
   4  9.515436 9.398666
   5  9.067212 8.995503
   6  9.028838 8.948561
   7  8.673814 8.771463
   8  8.762664 8.868634
   9  7.957576 7.926483
   10 8.016070 7.957696

Now I am trying to reproduce the result from parameters estimated by VSN
using
> coef(fit)[1,,]
            [,1]      [,2]
[1,] -0.08444849 -5.927967
[2,] -0.06787093 -5.957545
> offset <- coef(fit)[1,,1];
> scale <- exp(coef(fit)[1,,2]);
> ynorm_my = asinh(exprs(kidney)*scale + offset);
> ynorm_my[1:10,]
     channels
spots     green       red
   1  1.4820851 1.6139176
   2  1.2851048 1.4029668
   3  1.3588520 1.3584152
   4  1.3272734 1.2650499
   5  1.0353039 0.9986861
   6  0.9954236 0.9530607
   7  0.7626212 0.8400535
   8  0.8148209 0.8976601
   9  0.2661626 0.2376892
   10 0.3115130 0.2662458

which is clearly different from the result produced by VSN.  Could anybody
tell me what I have done wrong?  Thank you so much!

-- Leo

http://www.psi.toronto.edu/~ljlee/