Dear all,

 

I have a problem with loading matrix data into eset class object. The
data.frame is used to load tab-delimited processed data. But when I want to
run rma() method, there is always a error.

 

Microarray data is downloaded from ArrayExpress, since my PC is not powerful
to deal with raw data. I want to load processed data and then run it.

 

Below is the code:

 

library("affy")

library("limma")

arraydata=read.table(".\\E-MEXP-886.processed.1\\E-MEXP-886-processed-data-1
343526943.txt",sep="\t",quote="",row.names=1,header=TRUE)

phenoData=read.table("E-MEXP-886.sdrf.txt",sep="\t",quote="",header=TRUE,row
.names=1)

featureData=read.AnnotatedDataFrame("A-AFFY-23.adf.txt",sep="\t",quote="",he
ader=TRUE,fill=TRUE,skip=13)

 

#The blue part fetch Affymetrix:CHPSignal column of the processed data,
since the data format is as below:

#Scan REF   H_ataxin1WT-1753  H_ataxin1WT-1753  H_ataxin1WT-1753
H_ataxin1WT-1753      H_ataxin1WT-1753  H_ataxin1WT-1753  H_Ataxin1WT-1756
H_Ataxin1WT-1756  H_Ataxin1WT-1756  H_Ataxin1WT-1756  H_Ataxin1WT-1756
H_Ataxin1WT-1756  H_Ataxin1WT-1863  H_Ataxin1WT-1863  H_Ataxin1WT-1863
H_Ataxin1WT-1863  H_Ataxin1WT-1863  H_Ataxin1WT-1863  H_Ataxin1WT-1869
H_Ataxin1WT-1869  H_Ataxin1WT-1869  H_Ataxin1WT-1869  H_Ataxin1WT-1869
H_Ataxin1WT-1869  H_Ataxin1WT-1364  H_Ataxin1WT-1364  H_Ataxin1WT-1364
H_Ataxin1WT-1364  H_Ataxin1WT-1364  H_Ataxin1WT-1364  H_Ataxin1KO-1307
H_Ataxin1KO-1307  H_Ataxin1KO-1307  H_Ataxin1KO-1307  H_Ataxin1KO-1307
H_Ataxin1KO-1307  H_Ataxin1KO-1749  H_Ataxin1KO-1749  H_Ataxin1KO-1749
H_Ataxin1KO-1749  H_Ataxin1KO-1749  H_Ataxin1KO-1749  H_Ataxin1KO-1750
H_Ataxin1KO-1750  H_Ataxin1KO-1750  H_Ataxin1KO-1750  H_Ataxin1KO-1750
H_Ataxin1KO-1750  H_Ataxin1KO-1751  H_Ataxin1KO-1751  H_Ataxin1KO-1751
H_Ataxin1KO-1751  H_Ataxin1KO-1751  H_Ataxin1KO-1751  H_Ataxin1KO-1919
H_Ataxin1KO-1919  H_Ataxin1KO-1919  H_Ataxin1KO-1919  H_Ataxin1KO-1919
H_Ataxin1KO-1919

#Composite Element REF  Affymetrix:CHPProbeSetName    Affymetrix:CHPPairs
Affymetrix:CHPPairsUsed Affymetrix:CHPSignal    Affymetrix:CHPDetection
Affymetrix:CHPDetectionPvalue Affymetrix:CHPProbeSetName
Affymetrix:CHPPairs      Affymetrix:CHPPairsUsed Affymetrix:CHPSignal
Affymetrix:CHPDetection      Affymetrix:CHPDetectionPvalue
Affymetrix:CHPProbeSetName    Affymetrix:CHPPairs
Affymetrix:CHPPairsUsed Affymetrix:CHPSignal    Affymetrix:CHPDetection
Affymetrix:CHPDetectionPvalue Affymetrix:CHPProbeSetName
Affymetrix:CHPPairs      Affymetrix:CHPPairsUsed Affymetrix:CHPSignal
Affymetrix:CHPDetection      Affymetrix:CHPDetectionPvalue
Affymetrix:CHPProbeSetName    Affymetrix:CHPPairs
Affymetrix:CHPPairsUsed Affymetrix:CHPSignal    Affymetrix:CHPDetection
Affymetrix:CHPDetectionPvalue Affymetrix:CHPProbeSetName
Affymetrix:CHPPairs      Affymetrix:CHPPairsUsed Affymetrix:CHPSignal
Affymetrix:CHPDetection      Affymetrix:CHPDetectionPvalue
Affymetrix:CHPProbeSetName    Affymetrix:CHPPairs
Affymetrix:CHPPairsUsed Affymetrix:CHPSignal    Affymetrix:CHPDetection
Affymetrix:CHPDetectionPvalue Affymetrix:CHPProbeSetName
Affymetrix:CHPPairs      Affymetrix:CHPPairsUsed Affymetrix:CHPSignal
Affymetrix:CHPDetection      Affymetrix:CHPDetectionPvalue
Affymetrix:CHPProbeSetName    Affymetrix:CHPPairs
Affymetrix:CHPPairsUsed Affymetrix:CHPSignal    Affymetrix:CHPDetection
Affymetrix:CHPDetectionPvalue Affymetrix:CHPProbeSetName
Affymetrix:CHPPairs      Affymetrix:CHPPairsUsed Affymetrix:CHPSignal
Affymetrix:CHPDetection      Affymetrix:CHPDetectionPvalue

#Affymetrix:CompositeSequence:MOE430A:AFFX-BioB-5_at  AFFX-BioB-5_at    20
20    39.7      Present     0.00256     AFFX-BioB-5_at    20    20    60.1
Present     0.00125      AFFX-BioB-5_at    20    20    42.2  Present
0.00256     AFFX-BioB-5_at    20    20      93.5  Present     0.0003
AFFX-BioB-5_at    20    20    44.9  Present     0.00227      AFFX-BioB-5_at
20    20    75.3  Present     0.00097     AFFX-BioB-5_at    20    20
42.9  Present     0.00097     AFFX-BioB-5_at    20    20    53.7  Present
0.00159      AFFX-BioB-5_at    20    20    34.7  Present     0.00125
AFFX-BioB-5_at    20    20      93.8  Present     0.00034

#Affymetrix:CompositeSequence:MOE430A:AFFX-BioB-M_at  AFFX-BioB-M_at    20
20    61.1      Present     0.00017     AFFX-BioB-M_at    20    20    93.1
Present     0.00045      AFFX-BioB-M_at    20    20    70.2  Present
0.0002      AFFX-BioB-M_at    20    20      173.3 Present     5e-05
AFFX-BioB-M_at    20    20    59.7  Present     0.00013      AFFX-BioB-M_at
20    20    113.9 Present     0.00011     AFFX-BioB-M_at    20    20
75.5  Present     0.00039     AFFX-BioB-M_at    20    20    77.5  Present
0.00017      AFFX-BioB-M_at    20    20    68.7  Present     0.00026
AFFX-BioB-M_at    20    20      157.9 Present     7e-05

#Affymetrix:CompositeSequence:MOE430A:AFFX-BioB-3_at  AFFX-BioB-3_at    20
20    39      Present     0.00141     AFFX-BioB-3_at    20    20    49.6
Present     0.0011      AFFX-BioB-3_at    20    20    35.8  Present
0.00934     AFFX-BioB-3_at    20    20      69.6  Present     5e-05
AFFX-BioB-3_at    20    20    36    Present     0.00141      AFFX-BioB-3_at
20    20    73.2  Present     0.00066     AFFX-BioB-3_at    20    20
38.8  Present     0.0018      AFFX-BioB-3_at    20    20    39.1  Present
0.00097      AFFX-BioB-3_at    20    20    39.9  Present     0.00086
AFFX-BioB-3_at    20    20      75.9  Present     4e-05

 

sub_title=seq(1:10)*6-2

arraydata_pro=arraydata[,sub_title]

#replace the unmatched parts of names

sub_title_name=gsub("^H\\_|\\.[0-9]$","",colnames(arraydata[,sub_title]))

sub_title_name=gsub("\\.","-",sub_title_name)

colnames(arraydata_pro)=sub_title_name

#sort arraydata in the same order with phenoData

arraydata_pro=arraydata_pro[,order(colnames(arraydata_pro))]

#convert data.frame into AnnotatedDataFrame

phenoData=phenoData[order(row.names(phenoData)),]

phenoData=new("AnnotatedDataFrame", data=phenoData)

experimentData=read.MIAME("E-MEXP-886.idf.txt")

Eset=new("ExpressionSet", phenoData=phenoData, featureData=featureData,
experimentData=experimentData, exprs=as.matrix(arraydata_pro))

rEset=rma(Eset)

 

when I run the final line, it reported:

Error in function (classes, fdef, mtable)  : 

unable to find an inherited method for function "probeNames", for signature
"ExpressionSet"

 

I am really confusing about this error. Do you have the same experiences?

 

Thanks a lot!

 

Zhe

 

 

 

 


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