Displaying 3 results from an estimated 3 matches for "duplicatecorrelation".
2008 Mar 13
0
LIMMA: array spot summary options beyond duplicateCorrelation()
...Limma users
A quick question, I hope:
I have dual-channel spotted expression arrays in a simple loop design
(no dye swaps), viz:
1 vs reference
2 vs 1
3 vs 2
reference vs 3
There are 4 replicate spots for each probe on each array.
It seems as if getting meaningful spot summary results using
duplicateCorrelation() is not possible in my case as the spots are not
regularly spaced, and I don't *really* have enough arrays, no?
So then what are my other options in Limma to summarise replicated spots?
Thanks,
Quin
* *
* *
*Quin Wills*
*DPhil candidate*
* *
*Department of Statistics*
*University** of...
2007 Jul 30
0
problems in limma
...;normexp", four
warning messages appeared as "NaNs produced in: log(x)" (as you can see in
the program posted below). What does that mean? How will it effect the
final result? How could it be settled?
Question 2:
On my microarray, every probe has two replicates.During the process of
duplicateCorrelation, two warnings appear as "Too much damping -
convergence tolerance not achievable" (as you also can see in the program
posted below). What does it mean? Is there anything wrong with my data?
Question 3:
How to construct the design matrix is a puzzle to me. Here I constructed
the design ma...
2004 Nov 12
0
Design Matrix
...Treat_#4
The first slide (mice1.spot) and the second slide(mice2.spot) are
dye-swap. There is no common reference. There are 3 replicated spots of
each gene on each array (384 genes in total).
MA is an object of class marrayNorm, below is what I did.
>design <- c(1,-1,1,-1,1)
>cor <- duplicateCorrelation(MA,design,ndups=3)
>cor$consensus.correlation
[1] 0.506
>fit <- lmFit(MA,design,ndups=3,correlation=cor$consensus.correlation)
>fit <- eBayes(fit)
>topTable(fit,n=20,adjust="fdr")
The result is,
ID M A t P.Value B
348 -1.3 10.8 -3.98 0.577 -4.47
371 -1.91 11.5 -3.3...