I must have used the wrong version of CDF,when 'HuGene-1_0-st-v1,r3.cdf' was
used, the 'u' is correct.however, with next proceed step, there is still
some error.follows my code:
>library(aroma.affymetrix)
>verbose <- Arguments$getVerbose(-30); timestampOn(verbose)
>cdf<-AffymetrixCdfFile$byChipType("HuGene-1_0-st-v1",tags='r3',verbose=verbose)
>cs<-AffymetrixCelSet$byName("mydata",cdf=cdf,verbose=verbose)
>bc <- RmaBackgroundCorrection(cs)
>csBC <- process(bc,verbose=verbose)
>qn <- QuantileNormalization(csBC, typesToUpdate="pm")
>csN <- process(qn, verbose=verbose)
>cdfu <- getUniqueCdf(cdf,verbose=-80)
>csNU <- convertToUnique(csN,verbose=-20)
>plm <- RmaPlm(csNU)
>fit(plm, verbose=verbose)
>cls <- getNames(cs)
>library(FIRMAGene)
>hgnetaffx <-
read.csv("HuGene-1_0-st-v1.na25.hg18.transcript.csv",sep=",",skip=19,header=TRUE,comment.char="",stringsAsFactors=FALSE)
>probetab <-
read.table("HuGene-1_0-st-v1.probe.tab",sep="\t",header=TRUE,comment.char="",stringsAsFactors=FALSE)
>u <- which(getUnitNames(cdf) %in% hgnetaffx$probeset_id[hgnetaffx$category
== "main" & hgnetaffx$total_probes > 7 & hgnetaffx$total_probes < 200])
>fg <- FIRMAGene(plm, idsToUse=u, cls=cls)
>sampNames <- getNames(csNU)
>library(GenomeGraphs)
>mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL",
dataset="hsapiens_gene_ensembl", host="may2009.archive.ensembl.org")
>library(grid)
>getNames <- function(...) UseMethod("getNames") # clash of the 'getNames'
function
>top20 <- topSplices(fg,20)
> top20
ID Sample Score
15 8165686 317 45.33794
10 8179519 309 41.29322
14 8165684 317 35.23114
7 8118594 309 30.35256
18 8050548 320 28.96403
4 8165669 306 28.11474
1 7905691 306 27.08063
3 7932911 306 26.30232
5 8050548 308 26.24299
9 8168531 309 25.31600
20 8180100 320 24.01177
11 8180100 309 23.75232
19 8168531 320 23.43508
2 7923438 306 23.00059
8 8137979 309 22.60562
6 8111739 308 22.56581
13 8112007 317 22.05005
12 8111739 310 21.62827
17 8137979 319 20.86605
16 8057887 319 20.74905
> pdf("FIRMAGene_additional_file_1-plots.pdf",height=11,width=8.5)
> for(i in 1:nrow(top20)) {
+ col <- rep("black",33)
+ ww <- grep(top20$Sample[i],sampNames)
+ col[ ww ] <- "blue"
+ lwd <- c(1,3)[(col!="black")+1]
+ y <-
FIRMAGene::getDetails(plm,id=top20$ID[i],mart=mart,probesets=probetab,col=col,lwd=lwd)
+ y[[1]]@title <- paste( y[[1]]@title,
paste("blue",top20$Sample[i],sep="="), sep=" -- ")
+ if(length(y)>3) {
+ gdPlot(y)
+ }
+ }
error on getBM(geneSymbolId, filters = "ensembl_gene_id", values = gid, :
Values argument contains no data.
most of the script are from
http://bioinf.wehi.edu.au/folders/firmagene/sup3_04feb2010.R.
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