Thanks for your patience Neel, could you send me one of the files you are using, it would help me a lot working directly on the same data you are using. p.- De: Neel Aluru [mailto:naluru@whoi.edu] Enviado el: Thursday, June 17, 2010 1:49 PM Para: Pedro López Romero; bio c bioconductor Asunto: RE: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828. Thanks, Pedro. Here are the details you. I have noticed that what is in dd$genes and dd$other is different depending on whether I use read.maimages or readMicroRnaAFE function. I have pasted the details from both of them. The feature extraction software I used was version 9.3. Sincerely, Neel Session info () using read.maimages function > library("AgiMicroRna") > targets.micro=readTargets(infile="targets.txt", verbose=TRUE) Target File FileName Treatment GErep Subject 36_DMSO_1 36_DMSO_1.txt 36DMSO 1 1 36_DMSO_2 36_DMSO_2.txt 36DMSO 1 2 36_DMSO_3 36_DMSO_3.txt 36DMSO 1 3 36_TCDD_1 36_TCDD_1.txt 36TCDD 2 1 36_TCDD_2 36_TCDD_2.txt 36TCDD 2 2 36_TCDD_3 36_TCDD_3.txt 36TCDD 2 3 60_DMSO_1 60_DMSO_1.txt 60DMSO 3 1 60_DMSO_2 60_DMSO_2.txt 60DMSO 3 2 60_DMSO_3 60_DMSO_3.txt 60DMSO 3 3 60_TCDD_1 60_TCDD_1.txt 60TCDD 4 1 60_TCDD_2 60_TCDD_2.txt 60TCDD 4 2 60_TCDD_3 60_TCDD_3.txt 60TCDD 4 3 > ddaux=read.maimages(files=targets.micro$FileName,source="agilent", + other.columns=list(IsGeneDetected="gIsGeneDetected", + IsSaturated="gIsSaturated", + IsFeatNonUnifOF="gIsFeatNonUnifOL", + IsFeatPopnOL="gIsFeatPopnOL", + ChrCoord="chr_coord", BGKmd="gBGMedianSignal", + BGKus="gBGUsed"), + columns=list(Rf="gTotalGeneSignal", + Gf="gTotalProbeSignal", + Rb="gMeanSignal",Gb="gProcessedSignal"), verbose=TRUE,sep="\t",quote="") Read 36_DMSO_1.txt Read 36_DMSO_2.txt Read 36_DMSO_3.txt Read 36_TCDD_1.txt Read 36_TCDD_2.txt Read 36_TCDD_3.txt Read 60_DMSO_1.txt Read 60_DMSO_2.txt Read 60_DMSO_3.txt Read 60_TCDD_1.txt Read 60_TCDD_2.txt Read 60_TCDD_3.txt > names(ddaux) [1] "R" "G" "Rb" "Gb" "targets" "genes" "source" [8] "other" > names(ddaux$genes) [1] "Row" "Col" "Start" "Sequence" [5] "ProbeUID" "ControlType" "ProbeName" "GeneName" [9] "SystematicName" "Description" > names(ddaux$other) [1] "gIsGeneDetected" "gIsSaturated" "gIsFeatNonUnifOL" "gIsFeatPopnOL" [5] "gBGMedianSignal" "gBGUsed" Session Info () with AgiMicroRnaAFE function. > ddaux=readAgiMicroRnaAFE(targets.micro, verbose=TRUE) Error: could not find function "readAgiMicroRnaAFE" > ddaux=readMicroRnaAFE(targets.micro, verbose=TRUE) Read 36_DMSO_1.txt Read 36_DMSO_2.txt Read 36_DMSO_3.txt Read 36_TCDD_1.txt Read 36_TCDD_2.txt Read 36_TCDD_3.txt Read 60_DMSO_1.txt Read 60_DMSO_2.txt Read 60_DMSO_3.txt Read 60_TCDD_1.txt Read 60_TCDD_2.txt Read 60_TCDD_3.txt RGList: dd$R: 'gTotalGeneSignal' dd$G: 'gTotalProbeSignal' dd$Rb: 'gMeanSignal' dd$Gb: 'gProcessedSignal' > names(ddaux) [1] "R" "G" "Rb" "Gb" "targets" "genes" "other" > names(ddaux$genes) [1] "Sequence" "ProbeUID" "ControlType" > names(ddaux$other) [1] "gIsGeneDetected" "gIsSaturated" "gIsFeatNonUnifOL" "gIsFeatPopnOL" [5] "gBGMedianSignal" "gBGUsed" At 04:29 AM 6/17/2010, Pedro López Romero wrote: Hi Neel, I think your problem with the filtering function, is not the filtering itself but when the function tries to write an output. I am modifying this, so the user can choose whether or not they want to have an output file in the filtering step. In the meantime, can you tell me what you have in? names(dd), names(dd$genes) names(dd$genes) names(dd$other) What version of the Extractor are you using? p.- De: Neel Aluru [ mailto:naluru@whoi.edu ] Enviado el: Wednesday, June 16, 2010 10:54 PM Para: Richard Friedman; Pedro López Romero; bio c bioconductor Asunto: Re: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828. Hi Rich, Did you try filtering probes using FilterMicroRna function after removing the two columns. I am having difficulty in filtering probes. Thanks, Neel At 04:19 PM 6/16/2010, Richard Friedman wrote: Dear Pedro and List, My text files form Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828 has two extra columns which are not in GSE19232 Agilent human microRNA array v 2.0 (G44708) - "start" and "sequence". When these are deleted AgiMicroRNA works. I do not know if this is due to the array or software or processing options on the software. This clears up the problem with maMicroRna( which i have been writing you about. It would be nice if this could be taken into automatically in a future version of AgiMicroRNA, but this solves my porblem for now. Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet) Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ In Memoriam, George Scithers _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Neel Aluru Ph.D. Post doctoral Scholar Biology Department Redfield 304 (MS#32) Woods Hole Oceanographic Institution Woods Hole MA 02543 USA Phone: (508) 289-3607 [Office] 774-392-3727 [Cell] RID: A-7237-2009 ________________________________ *************** 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. Neel Aluru Ph.D. Post doctoral Scholar Biology Department Redfield 304 (MS#32) Woods Hole Oceanographic Institution Woods Hole MA 02543 USA Phone: (508) 289-3607 [Office] 774-392-3727 [Cell] RID: A-7237-2009 *************** 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]]