[BioC] contrast matrix warning

[scholz@Ag.arizona.edu]

Hi all,

I am getting a warning message when I create my contrast matrix (for a
six-membered loop design experiment) that I can't find any previous threads
about. The message reads:

Warning message:
use of NULL environment is deprecated

Here is a log of how it is generated, starting with a list of my targets file:

> targetsB
                    SlideNumber Name                FileName Cy3 Cy5
2005-11-18_B130high           1 B130 2005-11-18_B130high.gpr   A   B
2005-11-16_B121high           2 B121 2005-11-16_B121high.gpr   B   C
2005-11-15_B117high           3 B117 2005-11-15_B117high.gpr   C   D
2005-11-16_B119high           4 B119 2005-11-16_B119high.gpr   D   E
2005-11-18_B122high           5 B122 2005-11-18_B122high.gpr   E  RC
2005-11-17_B128high           6 B128 2005-11-17_B128high.gpr  RC   A
2005-11-17_B129high           7 B129 2005-11-17_B129high.gpr   A   C
2005-11-18_B131high           8 B131 2005-11-18_B131high.gpr   B   D
2005-11-16_B120high           9 B120 2005-11-16_B120high.gpr   C   E
2005-11-15_B118high          10 B118 2005-11-15_B118high.gpr   D  RC
2005-11-22_B137high          11 B137 2005-11-22_B137high.gpr   E   A
2005-11-18_B136high          12 B136 2005-11-18_B136high.gpr  RC   B

> designmatrix <- modelMatrix(targetsB, ref="RC")
Found unique target names:
 A B C D E RC

> designmatrix
                     A  B  C  D  E
2005-11-18_B130high -1  1  0  0  0
2005-11-16_B121high  0 -1  1  0  0
2005-11-15_B117high  0  0 -1  1  0
2005-11-16_B119high  0  0  0 -1  1
2005-11-18_B122high  0  0  0  0 -1
2005-11-17_B128high  1  0  0  0  0
2005-11-17_B129high -1  0  1  0  0
2005-11-18_B131high  0 -1  0  1  0
2005-11-16_B120high  0  0 -1  0  1
2005-11-15_B118high  0  0  0 -1  0
2005-11-22_B137high  1  0  0  0 -1
2005-11-18_B136high  0  1  0  0  0

> contrast.matrix = makeContrasts(A, A-B, A-C, A-E, B, B-C, B-E, C-E, C-D, E,
levels=designmatrix)
Warning message:
use of NULL environment is deprecated

> contrast.matrix
  A A - B A - C A - E B B - C B - E C - E C - D E
A 1     1     1     1 0     0     0     0     0 0
B 0    -1     0     0 1     1     1     0     0 0
C 0     0    -1     0 0    -1     0     1     1 0
D 0     0     0     0 0     0     0     0    -1 0
E 0     0     0    -1 0     0    -1    -1     0 1


What am I screwing up? Thanks in advance.

Matt

---------------------------------------------
College of Agriculture and Life Sciences Web Mail.
http://ag.arizona.edu