Question: A couple VSN related questions
0
12.0 years ago by
Leo J. LEE20
Leo J. LEE20 wrote:
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/
kidney vsn • 430 views
modified 12.0 years ago by Wolfgang Huber13k • written 12.0 years ago by Leo J. LEE20
Answer: A couple VSN related questions
0
12.0 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote: