Error using arrayQuality and Agilent txt files
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@f-javier-lopez-4285
Last seen 10.3 years ago
Dear All, I am trying to use the arrayQuality package with a set of two-color Agilent arrays (G2519F AMADID 014868 MOUSE 4x44), but I am just getting an error which I do not know how to overcome. Some details of the attempts we made: R version: 2.10.1 (also tried on 2.7.0) Packages version: arrayQuality_1.24.0, limma_3.2.3, RColorBrewer_1.0-2, gridBase_0.4-3, hexbin_1.22.0, lattice_0.18-3, convert_1.22.0, Biobase_2.6.1, marray_1.24.0 Raw data format: txt files obtained with the "Feature Extraction" Agilent software (You can have a look at the file header here: http://bioinformatics.fcrb.es/documentacion/header.txt). We first tried to use the agQuality function: > agQuality("US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt") [1] "Starting agQuality..." Reading ... ./US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt Error in slideQuality(gp, controlMatrix = controlMatrix, DEBUG = DEBUG) : dims [product 45018] do not match the length of object [0] It seemed that there were some kind of problem with file format, so we tried to do it by reading with read.maimages and then using maQualityPlots: > RG<-read.maimages("US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt ","agilent",columns = list(G = "gMedianSignal",Gb = "gBGMedianSignal",R ="rMedianSignal",Rb="rBGMedianSignal"),other.columns=c("gIsPosAndSigni f","rIsPosAndSignif"),annotation= c("Row","Col","ProbeUID","ProbeName","GeneName","accessions","Systemat icName","ControlType")) # This text file corresponds to one of the four arrays in the slide Read US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt > colnames(RG$genes)[2] <- "Column" > RG$genes$Block <- rep(1, length(RG$genes$ProbeName)) # There is only one block in the array > RG$printer <- getLayout(RG$genes) > maQualityPlots(RG) Error: dims [product 45018] do not match the length of object [45220] In addition: Warning messages: 1: In samplesub & which : longer object length is not a multiple of shorter object length 2: In samplesub & which & subset & good : longer object length is not a multiple of shorter object length It seems to be a problem with the array layout. There are only 45022 rows(probes) in the txt file from which 45018 are read by read.maimage, but also, the maximum row and column coordinates of the spots are 532 and 85 respectively. Multiplying 532x85 gives 45220, which is the expected size of the complete array. So, is it possible that the "Feature Extraction" software is filtering out some spots? Is it possible to run maQualityPlots if these spots are missing? Any clue? Thank you very much. Regards, F. Javier Lopez [[alternative HTML version deleted]]
arrayQuality arrayQuality • 1.4k views
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@valerie-obenchain-4275
Last seen 2.9 years ago
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Hi Javier, You are using an out of date version of R and Bioconductor. You should update to R 2.11 / BioC 2.6 or wait until next week when R 2.12 / BioC 2.7 will be available. http://www.bioconductor.org/install/index.html I would suggest using the arrayQualityMetrics package instead of arrayQuality. The arrayQuality package should have the functionality you are looking for along with helpful documentation and active maintainers. Let me know if you have problems. Valerie On 10/08/2010 05:24 AM, F. Javier L?pez wrote: > Dear All, > > I am trying to use the arrayQuality package with a set of two- color > Agilent arrays (G2519F AMADID 014868 MOUSE 4x44), but I am just getting an > error which I do not know how to overcome. Some details of the attempts we > made: > > R version: 2.10.1 (also tried on 2.7.0) > Packages version: arrayQuality_1.24.0, limma_3.2.3, RColorBrewer_1.0-2, > gridBase_0.4-3, hexbin_1.22.0, lattice_0.18-3, convert_1.22.0, > Biobase_2.6.1, marray_1.24.0 > Raw data format: txt files obtained with the "Feature Extraction" Agilent > software (You can have a look at the file header here: > http://bioinformatics.fcrb.es/documentacion/header.txt). > > We first tried to use the agQuality function: > > >> agQuality("US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt") >> > [1] "Starting agQuality..." > Reading ... ./US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt > Error in slideQuality(gp, controlMatrix = controlMatrix, DEBUG = DEBUG) : > dims [product 45018] do not match the length of object [0] > > It seemed that there were some kind of problem with file format, so we > tried to do it by reading with read.maimages and then using maQualityPlots: > > >> > RG<-read.maimages("US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.t xt","agilent",columns > = list(G = "gMedianSignal",Gb = "gBGMedianSignal",R > ="rMedianSignal",Rb="rBGMedianSignal"),other.columns=c("gIsPosAndSig nif","rIsPosAndSignif"),annotation= > c("Row","Col","ProbeUID","ProbeName","GeneName","accessions","System aticName","ControlType")) > # This text file corresponds to one of the four arrays in the slide > Read US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt > >> colnames(RG$genes)[2] <- "Column" >> RG$genes$Block <- rep(1, length(RG$genes$ProbeName)) # There is only one >> > block in the array > >> RG$printer <- getLayout(RG$genes) >> maQualityPlots(RG) >> > Error: dims [product 45018] do not match the length of object [45220] > In addition: Warning messages: > 1: In samplesub & which : > longer object length is not a multiple of shorter object length > 2: In samplesub & which & subset & good : > longer object length is not a multiple of shorter object length > > It seems to be a problem with the array layout. There are only 45022 > rows(probes) in the txt file from which 45018 are read by read.maimage, but > also, the maximum row and column coordinates of the spots are 532 and 85 > respectively. Multiplying 532x85 gives 45220, which is the expected size of > the complete array. So, is it possible that the "Feature Extraction" > software is filtering out some spots? Is it possible to run maQualityPlots > if these spots are missing? Any clue? > > Thank you very much. > > Regards, > > F. Javier Lopez > > [[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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Clarification my message below : The arrayQuality package should have the functionality you are looking for ... ^^^^^^^^^^^^^^^ should have read The arrayQualityMetrics package should have the functionality you are looking for ... ^^^^^^^^^^^^^^^^^^^^^^^^ Valerie On 10/12/2010 09:41 AM, Valerie Obenchain wrote: > Hi Javier, > > You are using an out of date version of R and Bioconductor. You should > update to R 2.11 / BioC 2.6 or wait until next week when R 2.12 / BioC > 2.7 will be available. > http://www.bioconductor.org/install/index.html > > I would suggest using the arrayQualityMetrics package instead of > arrayQuality. The arrayQuality package should have the functionality > you are looking for along with helpful documentation and active maintainers. > Let me know if you have problems. > > Valerie > > > > On 10/08/2010 05:24 AM, F. Javier L?pez wrote: > >> Dear All, >> >> I am trying to use the arrayQuality package with a set of two- color >> Agilent arrays (G2519F AMADID 014868 MOUSE 4x44), but I am just getting an >> error which I do not know how to overcome. Some details of the attempts we >> made: >> >> R version: 2.10.1 (also tried on 2.7.0) >> Packages version: arrayQuality_1.24.0, limma_3.2.3, RColorBrewer_1.0-2, >> gridBase_0.4-3, hexbin_1.22.0, lattice_0.18-3, convert_1.22.0, >> Biobase_2.6.1, marray_1.24.0 >> Raw data format: txt files obtained with the "Feature Extraction" Agilent >> software (You can have a look at the file header here: >> http://bioinformatics.fcrb.es/documentacion/header.txt). >> >> We first tried to use the agQuality function: >> >> >> >>> agQuality("US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt") >>> >>> >> [1] "Starting agQuality..." >> Reading ... ./US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt >> Error in slideQuality(gp, controlMatrix = controlMatrix, DEBUG = DEBUG) : >> dims [product 45018] do not match the length of object [0] >> >> It seemed that there were some kind of problem with file format, so we >> tried to do it by reading with read.maimages and then using maQualityPlots: >> >> >> >>> >>> >> RG<-read.maimages("US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1. txt","agilent",columns >> = list(G = "gMedianSignal",Gb = "gBGMedianSignal",R >> ="rMedianSignal",Rb="rBGMedianSignal"),other.columns=c("gIsPosAndSi gnif","rIsPosAndSignif"),annotation= >> c("Row","Col","ProbeUID","ProbeName","GeneName","accessions","Syste maticName","ControlType")) >> # This text file corresponds to one of the four arrays in the slide >> Read US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt >> >> >>> colnames(RG$genes)[2] <- "Column" >>> RG$genes$Block <- rep(1, length(RG$genes$ProbeName)) # There is only one >>> >>> >> block in the array >> >> >>> RG$printer <- getLayout(RG$genes) >>> maQualityPlots(RG) >>> >>> >> Error: dims [product 45018] do not match the length of object [45220] >> In addition: Warning messages: >> 1: In samplesub & which : >> longer object length is not a multiple of shorter object length >> 2: In samplesub & which & subset & good : >> longer object length is not a multiple of shorter object length >> >> It seems to be a problem with the array layout. There are only 45022 >> rows(probes) in the txt file from which 45018 are read by read.maimage, but >> also, the maximum row and column coordinates of the spots are 532 and 85 >> respectively. Multiplying 532x85 gives 45220, which is the expected size of >> the complete array. So, is it possible that the "Feature Extraction" >> software is filtering out some spots? Is it possible to run maQualityPlots >> if these spots are missing? Any clue? >> >> Thank you very much. >> >> Regards, >> >> F. Javier Lopez >> >> [[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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Hi all on a related note: the arrayQualityMetrics is since recently (currently only in the devel version) exploring ideas on how to make R-produced plots more interactive, using scripted svg, see e.g. http://www-huber.embl.de/users/whuber/arrayQualityMetrics- Reports/MLL/QMreport.html Figs. 4, 6 and 8. Best wishes Wolfgang Valerie Obenchain scripsit 12/10/10 18:51: > > Clarification my message below : > > The arrayQuality package should have the functionality you are looking > for ... > ^^^^^^^^^^^^^^^ > > should have read > > > The arrayQualityMetrics package should have the functionality you are > looking for ... > ^^^^^^^^^^^^^^^^^^^^^^^^ > > > Valerie > > > > On 10/12/2010 09:41 AM, Valerie Obenchain wrote: >> Hi Javier, >> >> You are using an out of date version of R and Bioconductor. You should >> update to R 2.11 / BioC 2.6 or wait until next week when R 2.12 / BioC >> 2.7 will be available. >> http://www.bioconductor.org/install/index.html >> >> I would suggest using the arrayQualityMetrics package instead of >> arrayQuality. The arrayQuality package should have the functionality >> you are looking for along with helpful documentation and active maintainers. >> Let me know if you have problems. >> >> Valerie >> >> >> >> On 10/08/2010 05:24 AM, F. Javier L?pez wrote: >> >>> Dear All, >>> >>> I am trying to use the arrayQuality package with a set of two- color >>> Agilent arrays (G2519F AMADID 014868 MOUSE 4x44), but I am just getting an >>> error which I do not know how to overcome. Some details of the attempts we >>> made: >>> >>> R version: 2.10.1 (also tried on 2.7.0) >>> Packages version: arrayQuality_1.24.0, limma_3.2.3, RColorBrewer_1.0-2, >>> gridBase_0.4-3, hexbin_1.22.0, lattice_0.18-3, convert_1.22.0, >>> Biobase_2.6.1, marray_1.24.0 >>> Raw data format: txt files obtained with the "Feature Extraction" Agilent >>> software (You can have a look at the file header here: >>> http://bioinformatics.fcrb.es/documentacion/header.txt). >>> >>> We first tried to use the agQuality function: >>> >>> >>> >>>> agQuality("US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt") >>>> >>>> >>> [1] "Starting agQuality..." >>> Reading ... ./US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt >>> Error in slideQuality(gp, controlMatrix = controlMatrix, DEBUG = DEBUG) : >>> dims [product 45018] do not match the length of object [0] >>> >>> It seemed that there were some kind of problem with file format, so we >>> tried to do it by reading with read.maimages and then using maQualityPlots: >>> >>> >>> >>>> >>>> >>> RG<-read.maimages("US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1 .txt","agilent",columns >>> = list(G = "gMedianSignal",Gb = "gBGMedianSignal",R >>> ="rMedianSignal",Rb="rBGMedianSignal"),other.columns=c("gIsPosAndS ignif","rIsPosAndSignif"),annotation= >>> c("Row","Col","ProbeUID","ProbeName","GeneName","accessions","Syst ematicName","ControlType")) >>> # This text file corresponds to one of the four arrays in the slide >>> Read US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt >>> >>> >>>> colnames(RG$genes)[2]<- "Column" >>>> RG$genes$Block<- rep(1, length(RG$genes$ProbeName)) # There is only one >>>> >>>> >>> block in the array >>> >>> >>>> RG$printer<- getLayout(RG$genes) >>>> maQualityPlots(RG) >>>> >>>> >>> Error: dims [product 45018] do not match the length of object [45220] >>> In addition: Warning messages: >>> 1: In samplesub& which : >>> longer object length is not a multiple of shorter object length >>> 2: In samplesub& which& subset& good : >>> longer object length is not a multiple of shorter object length >>> >>> It seems to be a problem with the array layout. There are only 45022 >>> rows(probes) in the txt file from which 45018 are read by read.maimage, but >>> also, the maximum row and column coordinates of the spots are 532 and 85 >>> respectively. Multiplying 532x85 gives 45220, which is the expected size of >>> the complete array. So, is it possible that the "Feature Extraction" >>> software is filtering out some spots? Is it possible to run maQualityPlots >>> if these spots are missing? Any clue? >>> >>> Thank you very much. >>> >>> Regards, >>> >>> F. Javier Lopez >>> >>> [[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 >> > > _______________________________________________ > 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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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@f-javier-lopez-4285
Last seen 10.3 years ago
Hi Valerie, Thank you very much for your answer. I have updated R and BioC and the problem still persists. I also had a look at the arrayQualityMetrics package, but I am quite interested in the quality-control measures calculated by agQuality that I cannot find in the arrayQualityMetrics. Thank you! Javier Hi Javier, > > You are using an out of date version of R and Bioconductor. You should > update to R 2.11 / BioC 2.6 or wait until next week when R 2.12 / BioC > 2.7 will be available. > http://www.bioconductor.org/install/index.html > > I would suggest using the arrayQualityMetrics package instead of > arrayQuality. The arrayQuality package should have the functionality > you are looking for along with helpful documentation and active > maintainers. > Let me know if you have problems. > > Valerie > [[alternative HTML version deleted]]
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On 10/14/2010 02:30 AM, F. Javier L?pez wrote: > Hi Valerie, > > Thank you very much for your answer. > > I have updated R and BioC and the problem still persists. Yes I get the errors too. There are several problems in the arrayQuality package and the maintainers have not updated the package in some time. I have cc'd them on this message in case they are interested in addressing them. > I also had a > look at the arrayQualityMetrics package, but I am quite interested in the > quality-control measures calculated by agQuality that I cannot find in the > arrayQualityMetrics. > I'm not sure which quality measures you are interested in. If arrayQualityMetrics doesn't have what you need you may want to look at the capabilities of the limma package. See the Linear Models for Microarray Data User's Guide, Chapter 5 Quality Control. http://bioconductor.org/help/bioc-views/2.7/bioc/html/limma.html The marray package would be another place to look. Valerie > Thank you! > > Javier > > > > > > Hi Javier, > >> You are using an out of date version of R and Bioconductor. You should >> update to R 2.11 / BioC 2.6 or wait until next week when R 2.12 / BioC >> 2.7 will be available. >> http://www.bioconductor.org/install/index.html >> >> I would suggest using the arrayQualityMetrics package instead of >> arrayQuality. The arrayQuality package should have the functionality >> you are looking for along with helpful documentation and active >> maintainers. >> Let me know if you have problems. >> >> Valerie >> >> > [[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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Hi Valerie, Thank you very much again. I will have a look at the limma and marray packages. I forgot to say I also tried using an marrayRaw object but the result was: > mraw <- read.Agilent(c("US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt", "US85003608_251486821883_S01_GE2-v5_10_Apr08_1_2.txt", "US85003608_251486821883_S01_GE2-v5_10_Apr08_1_3.txt", "US85003608_251486821883_S01_GE2-v5_10_Apr08_1_4.txt")) Reading ... ./US85003608_251486821883_S01_GE2-v5_10_Apr08_1_1.txt Reading ... ./US85003608_251486821883_S01_GE2-v5_10_Apr08_1_2.txt Reading ... ./US85003608_251486821883_S01_GE2-v5_10_Apr08_1_3.txt Reading ... ./US85003608_251486821883_S01_GE2-v5_10_Apr08_1_4.txt > maQualityPlots(mraw) [1] TRUE [1] TRUE [1] TRUE Error in .subset2(x, i, exact = exact) : attempt to select less than one element Best Wishes, Javier On 10/14/2010 02:30 AM, F. Javier L?pez wrote: > Hi Valerie, > > Thank you very much for your answer. > > I have updated R and BioC and the problem still persists. Yes I get the errors too. There are several problems in the arrayQuality package and the maintainers have not updated the package in some time. I have cc'd them on this message in case they are interested in addressing them. > I also had a > look at the arrayQualityMetrics package, but I am quite interested in the > quality-control measures calculated by agQuality that I cannot find in the > arrayQualityMetrics. > I'm not sure which quality measures you are interested in. If arrayQualityMetrics doesn't have what you need you may want to look at the capabilities of the limma package. See the Linear Models for Microarray Data User's Guide, Chapter 5 Quality Control. http://bioconductor.org/help/bioc-views/2.7/bioc/html/limma.html The marray package would be another place to look. Valerie [[alternative HTML version deleted]]
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