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 [[alternative HTML version deleted]]

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 *************** AVISO LEGAL *************** Este mensaje va dirigido, de manera exclusiva, a su destinatario y contiene información confidencial y sujeta al secreto profesional, cuya divulgación no está permitida por la ley. En caso de haber recibido este mensaje por error, le rogamos que, de forma inmediata, nos lo comunique mediante correo electrónico remitido a nuestra atención o a través del teléfono (+34 914531200) y proceda a su eliminación, así como a la de cualquier documento adjunto al mismo. Asimismo, le comunicamos que la distribución, copia o utilización de este mensaje, o de cualquier documento adjunto al mismo, cualquiera que fuera su finalidad, están prohibidas por la ley. Le informamos, como destinatario de este mensaje, que el correo electrónico y las comunicaciones por medio de Internet no permiten asegurar ni garantizar la confidencialidad de los mensajes transmitidos, así como tampoco su integridad o su correcta recepción, por lo que el CNIC no asume responsabilidad alguna por tales circunstancias. Si no consintiese la utilización del correo electrónico o de las comunicaciones vía Internet le rogamos nos lo comunique y ponga en nuestro conocimiento de manera inmediata. *************** LEGAL NOTICE ************** This message is intended exclusively for the person to whom it is addressed and contains privileged and confidential information protected from disclosure by law. If you are not the addressee indicated in this message, you should immediately delete it and any attachments and notify the sender by reply e-mail or by phone (+34 914531200). In such case, you are hereby notified that any dissemination, distribution, copying or use of this message or any attachments, for any purpose, is strictly prohibited by law. We hereby inform you, as addressee of this message, that e-mail and Internet do not guarantee the confidentiality, nor the completeness or proper reception of the messages sent and, thus, CNIC does not assume any liability for those circumstances. Should you not agree to the use of e-mail or to communications via Internet, you are kindly requested to notify us immediately. [[alternative HTML version deleted]]