[BioC] Normalization using control spots
Alison Waller
alison.waller at utoronto.ca
Fri Jul 17 18:09:00 CEST 2009
Hello all,
I have a set of 'boutique' Agilent arrays (ie. they are functional
gene arrays for which either a large or small number of gene can be
differenitally expressed). We have printed a few different sets of
control spots to use for within array normalization.
I have pasted by script below, and the error message and warnings.
Because of the warnings I thought that the set of control spots (6 out
of 3600 total) might be too small to fit a loess curve through so I
then tried with another 'control set" for which there are 220 spots .
And I still recieved the error " Error in qr.default(x) : NA/NaN/Inf
in foreign function call (arg 1) ", but there were no additional
warnings about too few degrees of freedom.
Any thoughts on why I'm recieving this error message?
Thanks,
Alison
Partial Script
>>>>>>
library(limma)
targets<-readTargets("EPBDIExprTargets.txt")
RG<-read.maimages(targets$FileName,source='genepix',wt.fun=wtflags(0.1))
spottypes<-readSpotTypes("SpotTypesEP.txt")
RGnm<-backgroundCorrect(RG,method='normexp')
RGnm$genes$Status<-controlStatus(spottypes,RG)
ControlSpots<-grep("Control",RGnm$genes$Status)
MAnmcntrl<-
normalizeWithinArrays(RGnm,method='control',controlspots=ControlSpots)
MAnmcntrlAqu<-normalizeBetweenArrays(MAnmcntrl,method='Aquantile')
Partial Output
>>>>>>>>>>>>>>
Corrected array 9
Red channel
Corrected array 1
Corrected array 2
Corrected array 3
Corrected array 4
Corrected array 5
Corrected array 6
Corrected array 7
Corrected array 8
Corrected array 9
Matching patterns for: ID
Found 3600 All
Found 6 Control
Setting attributes: values col cex
Error in qr.default(x) : NA/NaN/Inf in foreign function call (arg 1)
In addition: There were 50 or more warnings (use warnings() to see the
first 50)
> warnings()
Warning messages:
1: span too small. fewer data values than degrees of freedom.
2: zero-width neighborhood. make span bigger
3: zero-width neighborhood. make span bigger
4: zero-width neighborhood. make span bigger
5: zero-width neighborhood. make span bigger
6: zero-width neighborhood. make span bigger
7: zero-width neighborhood. make span bigger
8: Chernobyl! trL<k 0
9: Chernobyl! trL<k 0
10: span too small. fewer data values than degrees of freedom.
11: zero-width neighborhood. make span bigger
12: zero-width neighborhood. make span bigger
13: zero-width neighborhood. make span bigger
14: zero-width neighborhood. make span bigger
15: zero-width neighborhood. make span bigger
---------------------------------------------------------
Alison Waller Ph.D
alison.waller at utoronto.ca
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