Hi Heyi, 

 

readMicroRnaAFE uses the read.maimages function from limma. You can edit readMicroRnaAFE and remove the {ChrCoord="chr_coord"} in the “other.columns” list arguments. However, if you want to use RMA you will need the “gMeanSignal”. If you don´t have the gMeanSignal, change that argument in read.maimages and follow with your analysis using the gTotalGeneSignal. 

 

ddaux=read.maimages(files=targets$FileName,source="agilent",

                           other.columns=list(IsGeneDetected="gIsGeneDetected",

                                                                       IsSaturated="gIsSaturated",

                                                                       IsFeatNonUnifOF="gIsFeatNonUnifOL",

                                                                       IsFeatPopnOL="gIsFeatPopnOL",

                                                                       ChrCoord="chr_coord", 

                                                                       BGKmd="gBGMedianSignal",

                                                                       BGKus="gBGUsed"),

                         columns=list(Rf="gTotalGeneSignal",

                                                        Gf="gTotalProbeSignal",

                                                        Rb="gMeanSignal",

                                                        Gb="gProcessedSignal"),

                         verbose=TRUE,sep="\t",quote="")

 

p.- 

 

De: heyi xiao [mailto:xiaoheyiyh@yahoo.com] 
Enviado el: Monday, March 29, 2010 6:49 PM
Para: bioconductor@stat.math.ethz.ch
CC: Pedro López Romero
Asunto: readMicroRnaAFE function in AgiMicroR package

 

Hello Pedro,

I am using AgiMicroRna 1.0.0 to process my agilent miRNA microarray data. Agilent Feature Extraction Software v10.7 was used to extract the features. I would like to use readMicroRnaAFE function to read in the extracted feature data files. However, the error message says:

Error in readGenericHeader(fullname, columns = columns, sep = sep) : 

  Specified column headings not found in file

 

I check the feature data files, there are several relevant columns missing: gMeanSignal, gBGUsed, chr_coord. But I still want to use readMicroRnaAFE to create RGList so that AgiMicroRna can be used for further QC and analysis. Is it possible to do some small modification of the readMicroRnaAFE function to read in the data and still able to use the downstream utility (QC, RMA cross-array normalizationm, miRBase annotation linking etc) in AgiMicroRna? Thanks a lot for your input and help!

Heyi

 



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