Hi Qichengm.
Wrong dataset. That table was created using the Affy tissue panel, not the
Affy tissue mixture data.
Cheers,
Mark
On 2010-08-10, at 6:41 AM, qichengm wrote:
> 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
------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
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