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Paul, Cristina
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@paul-cristina-5211
Last seen 9.6 years ago
16 CEL files 4 treatments (one per chip- citrus chip) x 4
replications of each trt/chip with no subtreatments . Been googling
and reading etc but can't find a solution. I would like to subtract
the average reading from each probe 30K+ from the averaged reading of
each of the 3 other treatments before I compare/contrast the
remaining 3 trts for expression. We want to find out if there are
differences between all 3 plant pathogens and expression using this
chip to predict infectivity as well as which genes are up-regulated
and down regulated etc. Code below as far as I've gotten... Is this
the best way to proceed? Or other? 6 weeks and still at bottom of
Bioconductor and R learning curve.... Using R Studio with R 2.14 all
BiocLite packages are up to date.
R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-mingw32/x64 (64-bit)
library("affy")
list.celfiles()
Gdata <- ReadAffy()
Gdata
Loading required package: AnnotationDbi
AffyBatch object
size of arrays=984x984 features (23 kb)
cdf=Citrus (30395 affyids)
number of samples=16
number of genes=30395
annotation=citrus
notes=
pm(Gdata)[1:5, ]
Gdataeset <- expresso (Gdata, bgcorrect.method="rma",
normalize.method="quantiles", pmcorrect.method="mas",
summary.method="medianpolish")
sampleNames(Gdataeset)=sub("\\.CEL$","",sampleNames(Gdataeset))
exprs(Gdataeset)[1:20,]
targets<-readTargets("Gdata.txt", sep="")
targets
f<-paste(targets$Pathogen, sep="")
f<-factor(f)
f
Gdatadesign<-model.matrix(~0+f)
colnames(Gdatadesign)<-levels(f)
Gdatadesign
Virus bacterial Healthy phytoplasma
1 0 1 0 0
2 0 1 0 0
3 0 1 0 0
4 0 1 0 0
5 1 0 0 0
6 1 0 0 0
7 1 0 0 0
8 1 0 0 0
9 0 0 1 0
10 0 0 1 0
11 0 0 1 0
12 0 0 1 0
13 0 0 0 1
14 0 0 0 1
15 0 0 0 1
16 0 0 0 1
contrast.matrix<-makeContrasts(bacterial-Healthy, phytoplasma-Healthy,
virus-Healthy, levels=Gdatadesign)
contrast.matrix
Levels bacterial- Healthy phytoplasma - Healthy virus - Healthy
Virus 0 0 1
Bacteria 1 0 0
Healthy -1 -1 -1
phyto 0 1 0
as far as I've gotten.... But didn't want to put more effort if this
isn't the way to proceed.....
Thank you in advance....
Tina
If you are not part of the solution your are part of the
precipitate...
Cristina Paul
Citrus Quarantine Unit
USDA-ARS-BA-PSI-MPPL
Mailling address:
Bldg 004 Rm 118
Beltsville MD 20705
office: 301-504-7657
FAX: 301-504-5449
Cell: 240-286-6709
Physical Address:
Range 1 head house #6
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