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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