Entering edit mode
Brett Abrahams
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10
@brett-abrahams-1195
Last seen 9.6 years ago
Hello,
I would like to use limma to carry out single channel analyses on some
two
color data (to address comparisons that can't be made with standard
methods
and my unconnected experimental design). I'm able to get two color
analyses
to work nicely but run into problems when I try to run the single
channel
analysis using the 'lmscFit' function (as described in the March 9
2005
user's guide) .
Everything seems to work fine until I run 'intraspotCorrelation' which
results in a number of errors (see Point 1 below for input/output).
I've
looked into the versions of limma (Version: 1.8.22) and statmod
(Version:
1.1.0) but this doesn't seem to be the answer as both are current. Any
thoughts on why these error messages are being generated and what I
can do
to fix the problem would be much appreciated. Also, am I right in
thinking
the 'reml' errors I get refer to problems with only single genes? I
picked
this up from a previous post to the list but may have misinterpreted.
If I ignore the errors and carry on with the analysis through to the
topTable I get more results that I can't understand (see Point 2 below
input/output). What's confusing me here is that although results from
the
'decideTests' function seems to suggest that differentially expressed
genes
are present within each of the four contrasts I've specified, only one
of
the four corresponding topTables shows anything with significant p
values.
Amongst the contrasts without significant differences most p values
are >0.5 and all B values are negative. Any clarification would be
great.
Thanks in advance for this wonderful software and superb documentation
/
support.
Bret
Point 1
> corfit <- intraspotCorrelation(MA, design)
Loading required package: statmod
Attaching package 'statmod':
The following object(s) are masked from package:limma :
matvec vecmat
Warning messages:
1: reml: Max iterations exceeded in: remlscore(y, X, Z)
2: reml: Max iterations exceeded in: remlscore(y, X, Z)
3: reml: Max iterations exceeded in: remlscore(y, X, Z)
>
Point 2
Two groups (G1 and G2) with two tissues examined for each
> results <- decideTests(fit, method="nestedF")
> summary(results)
g1-g2 t1-t2 g1t2 - g2t2 g1t1-g2t1
-1 29 936 30 14
0 17866 16356 17861 17891
1 60 663 64 50
> topTable(fit3, coef=1, adjust="fdr")
> topTable(fit3, coef=1, adjust="fdr")
Status M A t P.Value B
15540 gene 0.4363826 8.514271 5.138324 0.6918086 -1.734635
10050 gene -0.3957220 9.904263 -4.802365 0.6918086 -1.936940
13504 gene 0.4280439 8.957909 4.492316 0.6918086 -2.136429
9953 gene 0.3380621 8.555516 4.486686 0.6918086 -2.140164
3266 gene 0.4737100 6.280065 4.478957 0.6918086 -2.145299
5596 gene 0.3738408 8.360172 4.327564 0.6918086 -2.247386
18159 gene -0.3860020 6.880403 -4.272878 0.6918086 -2.284962
6550 gene 0.4545545 7.901485 4.258022 0.6918086 -2.295233
8589 gene -0.4707301 7.850181 -4.227162 0.6918086 -2.316657
10149 gene 0.3387359 9.005838 4.216223 0.6918086 -2.324278
