AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828.
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Neel Aluru ▴ 460
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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 [[alternative HTML version deleted]]
miRNA Microarray Cancer microRNA miRNA Microarray Cancer microRNA • 1.0k views
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@richard-friedman-513
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Neel, I haven't tried filtering after removing the columns. I seem to remember that filtering worked on the test set, read in with the data funtion but not on my own data before I removed the columns. I have to give AgiMicroRNA a rest until tomorrow afternoon (EDT) to catch up on other things. A suggestion. 1. Download GSE19232 from GEO. 2. See if what you do works on that dataset, A. If it doesn't you are doing something incorrectly. B. If it does, try the same thing on your dataset. a. If it works on your setm fine. b. If it doesn't work on your set compare the column headings of GSE19232 to yorus and modify yours to conform to GSE19232. I hope that this helps, 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 at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ In Memoriam, George Scithers On Jun 16, 2010, at 4:54 PM, Neel Aluru wrote: > 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 at cancercenter.columbia.edu >> http://cancercenter.columbia.edu/~friedman/ >> >> In Memoriam, >> George Scithers >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at 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 >
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Neel Aluru ▴ 460
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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=""/>http://cancercenter.colu mbia.edu/~friedman/ > >In Memoriam, >George Scithers > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch ><https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">https://stat.ethz .ch/mailman/listinfo/bioconductor >Search the archives: ><http: news.gmane.org="" gmane.science.biology.informatics.conductor="">ht tp://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 [[alternative HTML version deleted]]
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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 <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]]
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Thanks Neel, I am working on your data, I know where the problem is. I have to modify (or even write a new function) to read the data in such a way that it is more flexible to the different data formats. I will let you know when I have this ready. 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 <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. 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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. 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@pedro-lopez-romero-1618
Last seen 7.1 years ago
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. [[alternative HTML version deleted]]
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Neel Aluru ▴ 460
@neel-aluru-3760
Last seen 4.8 years ago
United States
Thanks, Pedro. Looking forward to hearing from you. Sincerely, Neel At 03:20 AM 6/18/2010, Pedro López Romero wrote: >Thanks Neel, > >I am working on your data, I know where the >problem is. I have to modify (or even write a >new function) to read the data in such a way >that it is more flexible to the different data >formats. I will let you know when I have this ready. > >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=""/>http://cancercenter.colu mbia.edu/~friedman/ > >In Memoriam, >George Scithers > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch ><https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">https://stat.ethz .ch/mailman/listinfo/bioconductor >Search the archives: ><http: news.gmane.org="" gmane.science.biology.informatics.conductor="">ht tp://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. 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 [[alternative HTML version deleted]]
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Hi Neel and Richard, Thanks for your patience. I have slitghtly modified some code in the package, basically related to the way read.maimages is used. I have eliminated the use of the "chr_coord" column in some of the output files which it was what it was causing problems. Before these changes are made effective in the library, please, try this temporal solution: dd=read.maimages(files=targets$FileName,source="agilent", columns=list(Rf="gTotalGeneSignal", Gf="gTotalProbeSignal", Rb="gMeanSignal", Gb="gProcessedSignal"), other.columns=list(IsGeneDetected="gIsGeneDetected", IsSaturated="gIsSaturated", IsFeatNonUnifOF="gIsFeatNonUnifOL", IsFeatPopnOL="gIsFeatPopnOL", probe_mappings="probe_mappings", BGKmd="gBGMedianSignal", BGKus="gBGUsed"), annotation = c( "ControlType", "ProbeName","GeneName"), verbose=TRUE,sep="\t",quote="") before doing anything else, please check first that you have "probe_mappings" in the fifth position of "dd$other" > names(dd$other)[5] [1] "probe_mappings" Then, change the name of "probe_mappings" to the name that AgiMicroRna uses for this variable: > names(dd$other)[5] = "chr_coord" Then, use the rest of the functions as usual: ddTGS.rma = rmaMicroRna(dd, normalize = TRUE, background = FALSE) ddPROC = filterMicroRna(ddTGS.rma, dd, control = TRUE, IsGeneDetected = TRUE, wellaboveNEG = FALSE, limIsGeneDetected = 50, limNEG = 25, makePLOT = FALSE, targets, verbose = TRUE) Please, let me know if you still have any problem. Thanks p.- De: Neel Aluru [mailto:naluru@whoi.edu] Enviado el: Friday, June 18, 2010 1:44 PM Para: Pedro López Romero; bio c bioconductor Asunto: RE: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828. Thanks, Pedro. Looking forward to hearing from you. Sincerely, Neel At 03:20 AM 6/18/2010, Pedro López Romero wrote: Thanks Neel, I am working on your data, I know where the problem is. I have to modify (or even write a new function) to read the data in such a way that it is more flexible to the different data formats. I will let you know when I have this ready. p.- De: Neel Aluru [ mailto:naluru@whoi.edu <mailto:naluru@whoi.edu> ] Enviado el: Thursday, June 17, 2010 1:49 PM Para: Pedro López Romero; bio c bioconductor Asunto: RE: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828. Thanks, Pedro. Here are the details you. I have noticed that what is in dd$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> 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. 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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. 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. 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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. 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Hi Pedro, Thank you very much for fixing the problem. Everything works perfectly. I really appreciate your efforts. Sincerely, Neel On Jun 21, 2010, at 5:04 AM, Pedro López Romero wrote: > Hi Neel and Richard, > Thanks for your patience. > > I have slitghtly modified some code in the package, basically related to the way read.maimages is used. I have eliminated the use of the “chr_coord” column in some of the output files which it was what it was causing problems. Before these changes are made effective in the library, please, try this temporal solution: > > dd=read.maimages(files=targets$FileName,source="agilent", > columns=list(Rf="gTotalGeneSignal", > Gf="gTotalProbeSignal", > Rb="gMeanSignal", > Gb="gProcessedSignal"), > other.columns=list(IsGeneDetected="gIsGeneDetected", > IsSaturated="gIsSaturated", > IsFeatNonUnifOF="gIsFeatNonUnifOL", > IsFeatPopnOL="gIsFeatPopnOL", > probe_mappings="probe_mappings", > BGKmd="gBGMedianSignal", > BGKus="gBGUsed"), > annotation = c( "ControlType", "ProbeName","GeneName"), > verbose=TRUE,sep="\t",quote="") > > > before doing anything else, please check first that you have “probe_mappings” in the fifth position of “dd$other” > > names(dd$other)[5] > [1] "probe_mappings" > > Then, change the name of “probe_mappings” to the name that AgiMicroRna uses for this variable: > > names(dd$other)[5] = "chr_coord" > > Then, use the rest of the functions as usual: > > ddTGS.rma = rmaMicroRna(dd, normalize = TRUE, background = FALSE) > ddPROC = filterMicroRna(ddTGS.rma, > dd, > control = TRUE, > IsGeneDetected = TRUE, > wellaboveNEG = FALSE, > limIsGeneDetected = 50, > limNEG = 25, > makePLOT = FALSE, > targets, > verbose = TRUE) > > > Please, let me know if you still have any problem. Thanks > > p.- > > > De: Neel Aluru [mailto:naluru@whoi.edu] > Enviado el: Friday, June 18, 2010 1:44 PM > Para: Pedro López Romero; bio c bioconductor > Asunto: RE: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828. > > Thanks, Pedro. Looking forward to hearing from you. > > Sincerely, > Neel > > At 03:20 AM 6/18/2010, Pedro López Romero wrote: > > Thanks Neel, > > I am working on your data, I know where the problem is. I have to modify (or even write a new function) to read the data in such a way that it is more flexible to the different data formats. I will let you know when I have this ready. > > p.- > > De: Neel Aluru [ mailto:naluru@whoi.edu] > Enviado el: Thursday, June 17, 2010 1:49 PM > Para: Pedro López Romero; bio c bioconductor > Asunto: RE: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828. > > Thanks, Pedro. > > Here are the details you. I have noticed that what is in dd$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. 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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. > > > Neel Aluru Postdoctoral Scholar Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543 USA 508-289-3607 [[alternative HTML version deleted]]
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Pedro, I just got back to the microRNA today. Thank you very much! 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 at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ In Memoriam, George Scithers On Jun 21, 2010, at 5:04 AM, Pedro L?pez Romero wrote: > Hi Neel and Richard, > > Thanks for your patience. > > > > I have slitghtly modified some code in the package, basically > related to the way read.maimages is used. I have eliminated the use > of the "chr_coord" column in some of the output files which it was > what it was causing problems. Before these changes are made > effective in the library, please, try this temporal solution: > > > > dd=read.maimages(files=targets$FileName,source="agilent", > > columns=list(Rf="gTotalGeneSignal", > > > Gf="gTotalProbeSignal", > > > Rb="gMeanSignal", > > > Gb="gProcessedSignal"), > > > other.columns=list(IsGeneDetected="gIsGeneDetected", > > IsSaturated > ="gIsSaturated", > > IsFeatNonUnifOF > ="gIsFeatNonUnifOL", > > IsFeatPopnOL > ="gIsFeatPopnOL", > > > probe_mappings="probe_mappings", > > BGKmd > ="gBGMedianSignal", > > BGKus > ="gBGUsed"), > > annotation = c( "ControlType", > "ProbeName","GeneName"), > > verbose=TRUE,sep="\t",quote="") > > > > > > before doing anything else, please check first that you have > "probe_mappings" in the fifth position of "dd$other" > >> names(dd$other)[5] > > [1] "probe_mappings" > > > > Then, change the name of "probe_mappings" to the name that > AgiMicroRna uses for this variable: > >> names(dd$other)[5] = "chr_coord" > > > > Then, use the rest of the functions as usual: > > > > ddTGS.rma = rmaMicroRna(dd, normalize = TRUE, background = FALSE) > > ddPROC = filterMicroRna(ddTGS.rma, > > dd, > > control = TRUE, > > IsGeneDetected = TRUE, > > wellaboveNEG = FALSE, > > limIsGeneDetected = 50, > > limNEG = 25, > > makePLOT = FALSE, > > targets, > > verbose = TRUE) > > > > > > Please, let me know if you still have any problem. Thanks > > > > p.- > > > > > > De: Neel Aluru [mailto:naluru at whoi.edu] > Enviado el: Friday, June 18, 2010 1:44 PM > Para: Pedro L?pez Romero; bio c bioconductor > Asunto: RE: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse > miRNA Microarray Release 12.0 G4471A-021828. > > > > Thanks, Pedro. Looking forward to hearing from you. > > Sincerely, > Neel > > At 03:20 AM 6/18/2010, Pedro L?pez Romero wrote: > > > > Thanks Neel, > > I am working on your data, I know where the problem is. I have to > modify (or even write a new function) to read the data in such a > way that it is more flexible to the different data formats. I will > let you know when I have this ready. > > p.- > > De: Neel Aluru [ mailto:naluru at whoi.edu <mailto:naluru at="" whoi.edu=""> ] > Enviado el: Thursday, June 17, 2010 1:49 PM > Para: Pedro L?pez Romero; bio c bioconductor > Asunto: RE: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse > miRNA Microarray Release 12.0 G4471A-021828. > > Thanks, Pedro. > > Here are the details you. I have noticed that what is in dd$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 L?pez 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 at="" whoi.edu=""> mailto:naluru at whoi.edu] > Enviado el: Wednesday, June 16, 2010 10:54 PM > Para: Richard Friedman; Pedro L?pez 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 at cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > In Memoriam, > George Scithers > > _______________________________________________ > Bioconductor mailing list > Bioconductor at 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 informaci?n confidencial y sujeta al secreto profesional, > cuya divulgaci?n no est? permitida por la ley. En caso de haber > recibido este mensaje por error, le rogamos que, de forma inmediata, > nos lo comunique mediante correo electr?nico remitido a nuestra > atenci?n o a trav?s del tel?fono (+34 914531200) y proceda a su > eliminaci?n, as? como a la de cualquier documento adjunto al mismo. > Asimismo, le comunicamos que la distribuci?n, copia o utilizaci?n de > este mensaje, o de cualquier documento adjunto al mismo, cualquiera > que fuera su finalidad, est?n prohibidas por la ley. Le informamos, > como destinatario de este mensaje, que el correo electr?nico y las > comunicaciones por medio de Internet no permiten asegurar ni > garantizar la confidencialidad de los mensajes transmitidos, as? > como tampoco su integridad o su correcta recepci?n, por lo que el > CNIC no asume responsabilidad alguna por tales circunstancias. Si no > consintiese la utilizaci?n del correo electr?nico o de las > comunicaciones v?a 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 informaci?n confidencial y sujeta al secreto profesional, > cuya divulgaci?n no est? permitida por la ley. En caso de haber > recibido este mensaje por error, le rogamos que, de forma inmediata, > nos lo comunique mediante correo electr?nico remitido a nuestra > atenci?n o a trav?s del tel?fono (+34 914531200) y proceda a su > eliminaci?n, as? como a la de cualquier documento adjunto al mismo. > Asimismo, le comunicamos que la distribuci?n, copia o utilizaci?n de > este mensaje, o de cualquier documento adjunto al mismo, cualquiera > que fuera su finalidad, est?n prohibidas por la ley. Le informamos, > como destinatario de este mensaje, que el correo electr?nico y las > comunicaciones por medio de Internet no permiten asegurar ni > garantizar la confidencialidad de los mensajes transmitidos, as? > como tampoco su integridad o su correcta recepci?n, por lo que el > CNIC no asume responsabilidad alguna por tales circunstancias. Si no > consintiese la utilizaci?n del correo electr?nico o de las > comunicaciones v?a 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 informaci?n confidencial y sujeta al secreto profesional, > > cuya divulgaci?n no est? permitida por la ley. En caso de haber > > recibido este mensaje por error, le rogamos que, de forma inmediata, > > nos lo comunique mediante correo electr?nico remitido a nuestra > > atenci?n o a trav?s del tel?fono (+34 914531200) y proceda a su > > eliminaci?n, as? como a la de cualquier documento adjunto al mismo. > > Asimismo, le comunicamos que la distribuci?n, copia o utilizaci?n de > > este mensaje, o de cualquier documento adjunto al mismo, cualquiera > > que fuera su finalidad, est?n prohibidas por la ley. Le informamos, > > como destinatario de este mensaje, que el correo electr?nico y las > > comunicaciones por medio de Internet no permiten asegurar ni > > garantizar la confidencialidad de los mensajes transmitidos, as? como > > tampoco su integridad o su correcta recepci?n, por lo que el CNIC no > > asume responsabilidad alguna por tales circunstancias. Si no > > consintiese la utilizaci?n del correo electr?nico o de las > > comunicaciones v?a 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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To clarify, what you suggested worked perfectly! On Jun 30, 2010, at 3:36 PM, Richard Friedman wrote: > Pedro, > > I just got back to the microRNA today. > Thank you very much! > > 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 at cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > In Memoriam, > George Scithers > > > > On Jun 21, 2010, at 5:04 AM, Pedro L?pez Romero wrote: > >> Hi Neel and Richard, >> >> Thanks for your patience. >> >> >> >> I have slitghtly modified some code in the package, basically >> related to the way read.maimages is used. I have eliminated the use >> of the "chr_coord" column in some of the output files which it was >> what it was causing problems. Before these changes are made >> effective in the library, please, try this temporal solution: >> >> >> >> dd=read.maimages(files=targets$FileName,source="agilent", >> >> columns=list(Rf="gTotalGeneSignal", >> >> >> Gf="gTotalProbeSignal", >> >> >> Rb="gMeanSignal", >> >> >> Gb="gProcessedSignal"), >> >> >> other.columns=list(IsGeneDetected="gIsGeneDetected", >> >> IsSaturated >> ="gIsSaturated", >> >> IsFeatNonUnifOF >> ="gIsFeatNonUnifOL", >> >> IsFeatPopnOL >> ="gIsFeatPopnOL", >> >> >> probe_mappings="probe_mappings", >> >> BGKmd >> ="gBGMedianSignal", >> >> BGKus >> ="gBGUsed"), >> >> annotation = c( "ControlType", >> "ProbeName","GeneName"), >> >> verbose=TRUE,sep="\t",quote="") >> >> >> >> >> >> before doing anything else, please check first that you have >> "probe_mappings" in the fifth position of "dd$other" >> >>> names(dd$other)[5] >> >> [1] "probe_mappings" >> >> >> >> Then, change the name of "probe_mappings" to the name that >> AgiMicroRna uses for this variable: >> >>> names(dd$other)[5] = "chr_coord" >> >> >> >> Then, use the rest of the functions as usual: >> >> >> >> ddTGS.rma = rmaMicroRna(dd, normalize = TRUE, background = FALSE) >> >> ddPROC = filterMicroRna(ddTGS.rma, >> >> dd, >> >> control = TRUE, >> >> IsGeneDetected = TRUE, >> >> wellaboveNEG = FALSE, >> >> limIsGeneDetected = 50, >> >> limNEG = 25, >> >> makePLOT = FALSE, >> >> targets, >> >> verbose = TRUE) >> >> >> >> >> >> Please, let me know if you still have any problem. Thanks >> >> >> >> p.- >> >> >> >> >> >> De: Neel Aluru [mailto:naluru at whoi.edu] >> Enviado el: Friday, June 18, 2010 1:44 PM >> Para: Pedro L?pez Romero; bio c bioconductor >> Asunto: RE: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse >> miRNA Microarray Release 12.0 G4471A-021828. >> >> >> >> Thanks, Pedro. Looking forward to hearing from you. >> >> Sincerely, >> Neel >> >> At 03:20 AM 6/18/2010, Pedro L?pez Romero wrote: >> >> >> >> Thanks Neel, >> >> I am working on your data, I know where the problem is. I have to >> modify (or even write a new function) to read the data in such a >> way that it is more flexible to the different data formats. I will >> let you know when I have this ready. >> >> p.- >> >> De: Neel Aluru [ mailto:naluru at whoi.edu <mailto:naluru at="" whoi.edu=""> ] >> Enviado el: Thursday, June 17, 2010 1:49 PM >> Para: Pedro L?pez Romero; bio c bioconductor >> Asunto: RE: [BioC] AgiMicroRNA and Extra columns in Agilent Mouse >> miRNA Microarray Release 12.0 G4471A-021828. >> >> Thanks, Pedro. >> >> Here are the details you. I have noticed that what is in dd$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 L?pez 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 at="" whoi.edu=""> mailto:naluru at whoi.edu] >> Enviado el: Wednesday, June 16, 2010 10:54 PM >> Para: Richard Friedman; Pedro L?pez 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 at cancercenter.columbia.edu >> http://cancercenter.columbia.edu/~friedman/ >> >> In Memoriam, >> George Scithers >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at 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 informaci?n confidencial y sujeta al secreto profesional, >> cuya divulgaci?n no est? permitida por la ley. En caso de haber >> recibido este mensaje por error, le rogamos que, de forma >> inmediata, nos lo comunique mediante correo electr?nico remitido a >> nuestra atenci?n o a trav?s del tel?fono (+34 914531200) y proceda >> a su eliminaci?n, as? como a la de cualquier documento adjunto al >> mismo. Asimismo, le comunicamos que la distribuci?n, copia o >> utilizaci?n de este mensaje, o de cualquier documento adjunto al >> mismo, cualquiera que fuera su finalidad, est?n prohibidas por la >> ley. Le informamos, como destinatario de este mensaje, que el >> correo electr?nico y las comunicaciones por medio de Internet no >> permiten asegurar ni garantizar la confidencialidad de los mensajes >> transmitidos, as? como tampoco su integridad o su correcta >> recepci?n, por lo que el CNIC no asume responsabilidad alguna por >> tales circunstancias. Si no consintiese la utilizaci?n del correo >> electr?nico o de las comunicaciones v?a 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 informaci?n confidencial y sujeta al secreto profesional, >> cuya divulgaci?n no est? permitida por la ley. En caso de haber >> recibido este mensaje por error, le rogamos que, de forma >> inmediata, nos lo comunique mediante correo electr?nico remitido a >> nuestra atenci?n o a trav?s del tel?fono (+34 914531200) y proceda >> a su eliminaci?n, as? como a la de cualquier documento adjunto al >> mismo. Asimismo, le comunicamos que la distribuci?n, copia o >> utilizaci?n de este mensaje, o de cualquier documento adjunto al >> mismo, cualquiera que fuera su finalidad, est?n prohibidas por la >> ley. Le informamos, como destinatario de este mensaje, que el >> correo electr?nico y las comunicaciones por medio de Internet no >> permiten asegurar ni garantizar la confidencialidad de los mensajes >> transmitidos, as? como tampoco su integridad o su correcta >> recepci?n, por lo que el CNIC no asume responsabilidad alguna por >> tales circunstancias. Si no consintiese la utilizaci?n del correo >> electr?nico o de las comunicaciones v?a 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 informaci?n confidencial y sujeta al secreto profesional, >> >> cuya divulgaci?n no est? permitida por la ley. En caso de haber >> >> recibido este mensaje por error, le rogamos que, de forma inmediata, >> >> nos lo comunique mediante correo electr?nico remitido a nuestra >> >> atenci?n o a trav?s del tel?fono (+34 914531200) y proceda a su >> >> eliminaci?n, as? como a la de cualquier documento adjunto al mismo. >> >> Asimismo, le comunicamos que la distribuci?n, copia o utilizaci?n de >> >> este mensaje, o de cualquier documento adjunto al mismo, cualquiera >> >> que fuera su finalidad, est?n prohibidas por la ley. Le informamos, >> >> como destinatario de este mensaje, que el correo electr?nico y las >> >> comunicaciones por medio de Internet no permiten asegurar ni >> >> garantizar la confidencialidad de los mensajes transmitidos, as? como >> >> tampoco su integridad o su correcta recepci?n, por lo que el CNIC no >> >> asume responsabilidad alguna por tales circunstancias. Si no >> >> consintiese la utilizaci?n del correo electr?nico o de las >> >> comunicaciones v?a 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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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