Entering edit mode
Pie Muller
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110
@pie-muller-1349
Last seen 10.4 years ago
Dear Gordon and Bioconductor list members,
I am using limma to analyse an unlinked two-colour array experiment
consisting of 31 arrays (with 34,992 spots on each array) and 38
unique targets. I would like to separate the two channels to perform a
separate channel analysis using the function lmscFit() and tried to
follow the example given in the limma user's guide (see below) but
found that the "intraspotCorrelation()" gives me nothing but NaNs.
What could have gone wrong? There are no NaNs in either the M or A
values in my MAlist object. I suspect there might something wrong with
my design matrix as I noticed that by reducing the design matrix to
one single factor such as "design=matrix(rep(1,62), ncol=1)" I receive
a consensus correlation value back. However, there is still another
warning message "reml: Max iterations exceeded in: remlscore(y, X,
Z)". Does anyone have suggestions as to solve this problem?
In advance, many thanks for your support!
Pie
My target file:
> targets
Array Cy3 Cy5
1 2007-06-07_B2162-09.gpr F.168.C F.72.B
2 2007-06-07_B2162-13.gpr U.48.A U.24.A
3 2007-06-07_B2162-16.gpr F.24.E U.24.C
4 2007-06-07_B2162-20.gpr F.8.C U.8.C
5 2007-06-07_B2162-22.gpr U.24.A U.8.A
6 2007-06-15_B2162-02.gpr F.48.B F.24.D
7 2007-06-15_B2162-04.gpr U.72.A U.48.A
8 2007-06-15_B2162-05.gpr F.72.B F.48.B
9 2007-06-15_B2162-07.gpr F.48.C U.24.C
10 2007-06-15_B2162-10.gpr F.168.C U.8.B
11 2007-06-15_B2162-11.gpr U.168.A U.72.A
12 2007-06-15_B2162-19.gpr F.8.A U.168.A
13 2007-06-15_B2162-23.gpr F.72.C U.72.C
14 2007-06-15_B2162-25.gpr F.24.D F.8.B
15 2007-06-15_B2162-26.gpr F.168.D U.168.C
16 2007-09-26_B2165-05.gpr I.72.A I.48.A
17 2007-09-26_B2165-08.gpr I.24.A I.8.A
18 2007-09-26_B2165-12.gpr I.8.A F.168.B
19 2007-09-26_B2165-15.gpr I.8.A I.168.B
20 2007-09-26_B2165-18.gpr I.168.A I.72.A
21 2007-09-26_B2165-22.gpr I.48.A I.24.A
22 2007-09-28_B2165-02.gpr U.168.C I.168.C
23 2007-09-28_B2165-03.gpr I.168.C F.168.C
24 2007-09-28_B2165-04.gpr I.24.B F.24.D
25 2007-09-28_B2165-11.gpr I.72.B F.72.B
26 2007-09-28_B2165-14.gpr U.8.C I.8.C
27 2007-09-28_B2165-17.gpr U.72.C I.72.C
28 2007-09-28_B2165-19.gpr I.48.B F.48.B
29 2007-09-28_B2165-20.gpr U.48.C I.48.C
30 2007-09-28_B2165-23.gpr I.8.B F.8.B
31 2007-09-28_B2165-26.gpr U.24.C I.24.C
My code to generate the design matrix for single channel analysis:
# seperate channels
targets.sc=targetsA2C(targets)
u=uniquetargets.sc$Target)
f=factortargets.sc$Target, levels=u)
design=model.matrix(~0+f)
colnames(design)=u
The warnings produced by corfit=intraspotCorrelation(MA, design)
...
Warning message:
NaNs produced in: log(x)
Warning message:
NaNs produced in: log(x)
Warning message:
NaNs produced in: log(x)
Warning message:
NaNs produced in: log(x)
> corfit$consensus
[1] NaN
The warning produced if the design matrix is reduced to one single
factor:
> design=matrix(rep(1,62), ncol=1)
> corfit=intraspotCorrelation(MA, design)
Warning message:
reml: Max iterations exceeded in: remlscore(y, X, Z)
-------------------------------------
Dr Pie M?ller
Vector Group
Liverpool School of Tropical Medicine
Pembroke Place
Liverpool
L3 5QA
UK
Tel +44(0) 151 705 3225
Fax +44(0) 151 705 3369
http://www.liv.ac.uk/lstm
http://www.ivcc.com
