Hi,
I download the recent version of sup3_04feb2010.r, and made minor
changes to let it run, here is the difference:
$diff sup3_04feb2010.r sup3_04feb2010.r.orig
11,13c11
< #cdf<-AffymetrixCdfFile$byChipType("HuGene-1_0-st-
v1",verbose=verbose)
< chipType <- "HuGene-1_0-st-v1"
< cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
---
> cdf<-AffymetrixCdfFile$byChipType("HuGene-1_0-st-v1",verbose=verbose)
16c14
< cs<-AffymetrixCelSet
$byName("TisMix_WTGene1C",cdf=cdf,verbose=verbose)
---
> cs<-AffymetrixCelSet$byName("tissues",cdf=cdf,verbose=verbose)
35,39c33,34
< #hgnetaffx <- read.csv("HuGene-1_0-st-
v1.na25.hg18.transcript.csv",sep=",",skip=19,header=TRUE,comment.char="",stringsAsFactors=FALSE)
< hgnetaffx <- read.csv("annotationData/chipTypes/HuGene-1_0-st-v1/
HuGene-1_0-st-
v1.na30.hg19.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)
< probetab <- read.table("annotationData/chipTypes/HuGene-1_0-st-v1/
HuGene-1_0-st-
v1.hg19.probe.tab",sep="\t",header=TRUE,comment.char="",stringsAsFactors=FALSE)
---
> 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)
Top 20 hits are different from those in the FirmaGene paper
"ID","Sample","Score","Symbol"
"7934979","TisMix_mix9",49.0412085693221,"ANKRD1"
"7987315","TisMix_mix9",48.5685310739171,"ACTC1"
"8023889","TisMix_mix1",37.4399023091527,"MBP"
"8060963","TisMix_mix1",36.0242843230823,"SNAP25"
"7947099","TisMix_mix9",35.1698682900308,"CSRP3"
"7912520","TisMix_mix9",34.2770659572940,"NPPB"
"7929653","TisMix_mix9",31.4139588184231,"ANKRD2"
"8096959","TisMix_mix1",30.9351264815591,"ANK2"
"7912692","TisMix_mix9",30.7020787308514,"HSPB7"
"7957338","TisMix_mix1",30.6749548684879,"SYT1"
"8169061","TisMix_mix1",29.9989728237812,"PLP1"
"8087925","TisMix_mix9",29.4092542289276,"TNNC1"
"7930208","TisMix_mix1",29.002191135071,"INA"
"8046062","TisMix_mix9",28.5683689224915,"XIRP2"
"8109663","TisMix_mix1",28.3206965639246,"GABRA1"
"7982018","TisMix_mix1",28.3138146218297,"SNORD115-6"
"7924910","TisMix_mix9",28.2833712932546,"ACTA1"
"7982090","TisMix_mix1",27.4880562975114,"SNORD115-42"
"8103789","TisMix_mix1",27.399249112706,"GPM6A"
"7982008","TisMix_mix1",25.0039468447955,"SNORD115-1"
Could you please tell me where I am wrong ?
Thanks,
Qichengm
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