[BioC] illumina code

[Matthew Vitalone]

Hi all,

I was just wanted someone to have a look at my rcode to see if it is 
correct. This analysis (Illumina) arrays is comparing CAN vs No-CAN via 
a common reference. I have 8 pts with CAN, 13 pts without CAN, 3 ref 
along with 2 with fibrosis only (FO) and  2 with no histology (NB). The 
contrast i wanted to make is CAN vs No-CAN via CAN vs Ref and NoCAN vs 
Ref. Ignoring the FO and NB. I have put this code together from the 
Limma and beadarry guides and general internet published documents. I 
get a diff exp list at the end, I just wanted to check to see if the 
analysis is correct, so I can trust the final diff exp list. Sorry, if 
the code i messy, I have taught myself to use Limma and R.

Thank you,
Matt

Rcode:

*library(limma)*

*library(beadarray)*

<>*setwd("d:/Illumina_results/expset")*  <>*

BSData = readBeadSummaryData("expset-QCgood-4.txt", qcFile=NULL, 
sampleSheet=NULL,sep="\t",skip=8, ProbeID="PROBE_ID", columns = 
list(exprs = "AVG_Signal", se.exprs="BEAD_STDERR", NoBeads = 
"Avg_NBEADS", Detection="Detection Pval"), dec=".")*  <>*

BSData.qspline = normaliseIllumina(BSData, method="qspline", 
transform=NULL)*

*BSData.norm = BSData.qspline*

<>*design = 
model.matrix(~-1+factor(c(1,3,4,1,1,1,2,2,3,3,1,2,1,2,1,1,1,2,1,2,4,5,1,5 
))) *

*colnames(design) = c("NC", "C", "Ref", "FO", "NB")*

 <>*design[**1:24**,1:5]*  <>*

fit = lmFit(log2(exprs(BSData.norm)), design)*

*con.matrix = makeContrasts (CvsNC = C-NC, CvsRef = C-Ref, NCvsRef = 
NC-Ref, levels = design)

*

<>*fit2 = contrasts.fit(fit, con.matrix)*

*ebFit = eBayes(fit2)*

*options(digits=3)*

*tt = topTable(ebFit, n=dim(fit)[1], adjust="fdr")*

*write.table(tt, "d:/Illumina_results/expset/3mCAN_b.txt ", row.names=F, 
quote=F, sep="\t")*


-- 
Matthew Vitalone B.Sc (Hons) PhD(progress)
NHMRC Centre for Clinical Research Excellence in Renal Medicine
Centre For Transplant and Renal Research
Transplant Laboratory (Room 2175), Clinical Sciences
Westmead Millennium Institute
Darcy Road, Westmead, NSW, 2145.
Sydney, Australia.

Phone: (+61-2) 9845 8906
Mobile: 0416 041783
Hosp. Page: 27147
Fax: (+61-2) 9633 9351
Email: matthew_vitalone at wmi.usyd.edu.au 
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