Question: Agi4x44Preprocess - error on read.AgilentFE fucntion
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5.7 years ago by
Guest User12k
Guest User12k wrote:
Hello everybody! I'm using Agi4x44Preprocess package to deal with pre processing Agilent single color 4x44 whole mouse genome array, which data were obtained using feature extraction software. The problem is that I can't download my data with the function read.AgilentFE, I got an error - showed below - and the script just stop and, instead mine, the author's example data is imported... I used read.maimages function of the package limma as an alternative, but I really would like to know what is wrong using read.AglentFE. Regards, Amanda -- output of sessionInfo(): > targets <- read.targets(infile="targets.txt") Target File FileName Treatment Gerep CT1 CT1.txt CT 1 CT2 CT2.txt CT 1 CT3 CT3.txt CT 1 TT1 TT1.txt TT 2 TT2 TT2.txt TT 2 TT3 TT3.txt TT 2 PT1 PT1.txt PT 3 PT2 PT2.txt PT 3 PT3 PT3.txt PT 3 > dd <-read.AgilentFE(targets,makePLOT=TRUE) Read CT1.txt Read CT2.txt Read CT3.txt Read TT1.txt Read TT2.txt Read TT3.txt Read PT1.txt Read PT2.txt Read PT3.txt INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord SCANN THE DATA USING AFE 9.5.3.1 Erro em read.AgilentFE(targets, makePLOT = TRUE) : the script will stop now -- Sent via the guest posting facility at bioconductor.org.
limma agi4x44preprocess • 755 views
ADD COMMENTlink modified 5.7 years ago by James W. MacDonald51k • written 5.7 years ago by Guest User12k
Answer: Agi4x44Preprocess - error on read.AgilentFE fucntion
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gravatar for James W. MacDonald
5.7 years ago by
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James W. MacDonald51k wrote:
Hi Amanda, On 1/23/2014 12:04 PM, Amanda F A Riccardi [guest] wrote: > Hello everybody! > > I'm using Agi4x44Preprocess package to deal with pre processing Agilent single color 4x44 whole mouse genome array, which data were obtained using feature extraction software. > The problem is that I can't download my data with the function read.AgilentFE, I got an error - showed below - and the script just stop and, instead mine, the author's example data is imported... I used read.maimages function of the package limma as an alternative, but I really would like to know what is wrong using read.AglentFE. > Regards, > Amanda > > -- output of sessionInfo(): > >> targets <- read.targets(infile="targets.txt") > > Target File > FileName Treatment Gerep > CT1 CT1.txt CT 1 > CT2 CT2.txt CT 1 > CT3 CT3.txt CT 1 > TT1 TT1.txt TT 2 > TT2 TT2.txt TT 2 > TT3 TT3.txt TT 2 > PT1 PT1.txt PT 3 > PT2 PT2.txt PT 3 > PT3 PT3.txt PT 3 > >> dd <-read.AgilentFE(targets,makePLOT=TRUE) > Read CT1.txt > Read CT2.txt > Read CT3.txt > Read TT1.txt > Read TT2.txt > Read TT3.txt > Read PT1.txt > Read PT2.txt > Read PT3.txt > INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord > SCANN THE DATA USING AFE 9.5.3.1 ^^^^^^^^^ That is supposed to be your hint. What it means is that the sequence and chromosome coordinate data are not available, and that you should use Agilent Feature Extraction version 9.5.3.1 (or higher, I presume). If you don't have these data available, read.AgilentFE() will fail, as this test is hard-coded into the function. In other words, unless you upgrade your AFE version, you will have to use read.maimages() directly. Best, Jim > Erro em read.AgilentFE(targets, makePLOT = TRUE) : > the script will stop now > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 5.7 years ago by James W. MacDonald51k
Answer: Agi4x44Preprocess - error on read.AgilentFE fucntion
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gravatar for James W. MacDonald
5.7 years ago by
United States
James W. MacDonald51k wrote:
Hi Amanda, Please don't take conversations off-list (e.g., use Reply-All). On 1/23/2014 1:21 PM, amandafassis at usp.br wrote: > Thank you very much James! > > In fact I had already done a test using readmaimages from limma > package that worked very well inputting the data. : > > >library(limma) > > targets<-readTargets("targets.txt") > > >x<-read.maimages(targets, source="agilent", green.only=TRUE) > > But I couldn't go further on pre processing data wijt Agi4x44 because > I got another error: > > Erro em BGandNorm(x, BGmethod = normexp, NORMmethod = quantile, > foreground = MedianSignal, : > 'input' must be a RGList > > It seems that this package doesn't deal with single channel arrays... > Do you know something about that? I haven't used Agi4x44PreProcess for a while now. I am not that familiar with the Agilent 4x44 arrays - I have only used the Salmonid arrays designed by the Koop lab, which are single color, so maybe there are two color 4x44 arrays out there that I don't know about. But if you look at the code for read.AgilentFE and BGandNorm, you can see that the author has done a bunch of work to stuff the results into an RGList, and then work within that framework. In other words, Agi4x44PreProcess sort of pretends that these arrays are two color even if they are not, and has to do a bunch of extra work because there is only data in one channel. That is weird to me, as there is the EList structure, which is designed specifically for single color spotted arrays, but maybe Agi4x44PreProcess precedes the addition of EList to limma. I really don't know. But anyway, it is much easier and (to me) safer to just use limma directly: x <- read.maimages(targets, source = "agilent", green.only = TRUE) x <- backgroundCorrect(x, method = "normexp") x <- normalizeBetweenArrays(x, method = "quantile") Then you can filter out probes that are just above background if you like, and go directly on to model fitting. There is a worked example for these arrays in the limma User's Guide, starting on page 110 that you might like to read. Best, Jim > > > Amanda Freire de Assis, MSc > Molecular Immunogenetics Group > University of S?o Paulo > Av. Bandeirantes, 3900 > 14049-900 - Ribeir?o Preto - Brazil > +55 16 36023246 > > ----- James W. MacDonald <jmacdon at="" uw.edu=""> escreveu: > > Hi Amanda, > > > > On 1/23/2014 12:04 PM, Amanda F A Riccardi [guest] wrote: > > > Hello everybody! > > > > > > I'm using Agi4x44Preprocess package to deal with pre processing > Agilent single color 4x44 whole mouse genome array, which data were > obtained using feature extraction software. > > > The problem is that I can't download my data with the function > read.AgilentFE, I got an error - showed below - and the script just > stop and, instead mine, the author's example data is imported... I > used read.maimages function of the package limma as an alternative, > but I really would like to know what is wrong using read.AglentFE. > > > Regards, > > > Amanda > > > > > > -- output of sessionInfo(): > > > > > >> targets <- read.targets(infile="targets.txt") > > > > > > Target File > > > FileName Treatment Gerep > > > CT1 CT1.txt CT 1 > > > CT2 CT2.txt CT 1 > > > CT3 CT3.txt CT 1 > > > TT1 TT1.txt TT 2 > > > TT2 TT2.txt TT 2 > > > TT3 TT3.txt TT 2 > > > PT1 PT1.txt PT 3 > > > PT2 PT2.txt PT 3 > > > PT3 PT3.txt PT 3 > > > > > >> dd <-read.AgilentFE(targets,makePLOT=TRUE) > > > Read CT1.txt > > > Read CT2.txt > > > Read CT3.txt > > > Read TT1.txt > > > Read TT2.txt > > > Read TT3.txt > > > Read PT1.txt > > > Read PT2.txt > > > Read PT3.txt > > > INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord > > > SCANN THE DATA USING AFE 9.5.3.1 > > > > ^^^^^^^^^ That is supposed to be your hint. What it means is that the > > sequence and chromosome coordinate data are not available, and that you > > should use Agilent Feature Extraction version 9.5.3.1 (or higher, I > > presume). > > > > If you don't have these data available, read.AgilentFE() will fail, as > > this test is hard-coded into the function. In other words, unless you > > upgrade your AFE version, you will have to use read.maimages() directly. > > > > Best, > > > > Jim > > > > > > > Erro em read.AgilentFE(targets, makePLOT = TRUE) : > > > the script will stop now > > > > > > > > > -- > > > Sent via the guest posting facility at bioconductor.org. > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at r-project.org > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > > James W. MacDonald, M.S. > > Biostatistician > > University of Washington > > Environmental and Occupational Health Sciences > > 4225 Roosevelt Way NE, # 100 > > Seattle WA 98105-6099 > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 5.7 years ago by James W. MacDonald51k
Dear James, thanks for the support and good remarks. Amanda Freire de Assis, MSc Molecular Immunogenetics Group University of São Paulo Av. Bandeirantes, 3900 14049-900 - Ribeirão Preto - Brazil +55 16 36023246 ----- James W. MacDonald <jmacdon@uw.edu> escreveu: > Hi Amanda, > > Please don't take conversations off-list (e.g., use Reply-All). > > On 1/23/2014 1:21 PM, amandafassis@usp.br wrote: > > Thank you very much James! > > > > In fact I had already done a test using readmaimages from limma > > package that worked very well inputting the data. : > > > > >library(limma) > > > targets<-readTargets("targets.txt") > > > > >x<-read.maimages(targets, source="agilent", green.only=TRUE) > > > > But I couldn't go further on pre processing data wijt Agi4x44 because > > I got another error: > > > > Erro em BGandNorm(x, BGmethod = normexp, NORMmethod = quantile, > > foreground = MedianSignal, : > > 'input' must be a RGList > > > > It seems that this package doesn't deal with single channel arrays... > > Do you know something about that? > > I haven't used Agi4x44PreProcess for a while now. I am not that familiar > with the Agilent 4x44 arrays - I have only used the Salmonid arrays > designed by the Koop lab, which are single color, so maybe there are two > color 4x44 arrays out there that I don't know about. But if you look at > the code for read.AgilentFE and BGandNorm, you can see that the author > has done a bunch of work to stuff the results into an RGList, and then > work within that framework. In other words, Agi4x44PreProcess sort of > pretends that these arrays are two color even if they are not, and has > to do a bunch of extra work because there is only data in one channel. > > That is weird to me, as there is the EList structure, which is designed > specifically for single color spotted arrays, but maybe > Agi4x44PreProcess precedes the addition of EList to limma. I really > don't know. But anyway, it is much easier and (to me) safer to just use > limma directly: > > x <- read.maimages(targets, source = "agilent", green.only = TRUE) > x <- backgroundCorrect(x, method = "normexp") > x <- normalizeBetweenArrays(x, method = "quantile") > > Then you can filter out probes that are just above background if you > like, and go directly on to model fitting. There is a worked example for > these arrays in the limma User's Guide, starting on page 110 that you > might like to read. > > Best, > > Jim > > > > > > > > Amanda Freire de Assis, MSc > > Molecular Immunogenetics Group > > University of São Paulo > > Av. Bandeirantes, 3900 > > 14049-900 - Ribeirão Preto - Brazil > > +55 16 36023246 > > > > ----- James W. MacDonald escreveu: > > > Hi Amanda, > > > > > > On 1/23/2014 12:04 PM, Amanda F A Riccardi [guest] wrote: > > > > Hello everybody! > > > > > > > > I'm using Agi4x44Preprocess package to deal with pre processing > > Agilent single color 4x44 whole mouse genome array, which data were > > obtained using feature extraction software. > > > > The problem is that I can't download my data with the function > > read.AgilentFE, I got an error - showed below - and the script just > > stop and, instead mine, the author's example data is imported... I > > used read.maimages function of the package limma as an alternative, > > but I really would like to know what is wrong using read.AglentFE. > > > > Regards, > > > > Amanda > > > > > > > > -- output of sessionInfo(): > > > > > > > >> targets <- read.targets(infile="targets.txt") > > > > > > > > Target File > > > > FileName Treatment Gerep > > > > CT1 CT1.txt CT 1 > > > > CT2 CT2.txt CT 1 > > > > CT3 CT3.txt CT 1 > > > > TT1 TT1.txt TT 2 > > > > TT2 TT2.txt TT 2 > > > > TT3 TT3.txt TT 2 > > > > PT1 PT1.txt PT 3 > > > > PT2 PT2.txt PT 3 > > > > PT3 PT3.txt PT 3 > > > > > > > >> dd <-read.AgilentFE(targets,makePLOT=TRUE) > > > > Read CT1.txt > > > > Read CT2.txt > > > > Read CT3.txt > > > > Read TT1.txt > > > > Read TT2.txt > > > > Read TT3.txt > > > > Read PT1.txt > > > > Read PT2.txt > > > > Read PT3.txt > > > > INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord > > > > SCANN THE DATA USING AFE 9.5.3.1 > > > > > > ^^^^^^^^^ That is supposed to be your hint. What it means is that the > > > sequence and chromosome coordinate data are not available, and that you > > > should use Agilent Feature Extraction version 9.5.3.1 (or higher, I > > > presume). > > > > > > If you don't have these data available, read.AgilentFE() will fail, as > > > this test is hard-coded into the function. In other words, unless you > > > upgrade your AFE version, you will have to use read.maimages() directly. > > > > > > Best, > > > > > > Jim > > > > > > > > > > Erro em read.AgilentFE(targets, makePLOT = TRUE) : > > > > the script will stop now > > > > > > > > > > > > -- > > > > Sent via the guest posting facility at bioconductor.org. > > > > > > > > _______________________________________________ > > > > Bioconductor mailing list > > > > Bioconductor@r-project.org > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > > > James W. MacDonald, M.S. > > > Biostatistician > > > University of Washington > > > Environmental and Occupational Health Sciences > > > 4225 Roosevelt Way NE, # 100 > > > Seattle WA 98105-6099 > > > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > [[alternative HTML version deleted]]
ADD REPLYlink written 5.7 years ago by amandafassis@usp.br20
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