Question: Problem with ABarray package
0
gravatar for Alison Ziesel
12.7 years ago by
United States
Alison Ziesel60 wrote:
Hello Conductors, I have very recently started using R and BioConductor to help with array analysis for my supervisor and co-workers. I must confess that I am very much a beginner and I apologize in advance if the question posed is too basic for this list. The first and only BioC package I've been using is ABarray. After getting R working and running the BiocLite.R install package for BioConductor, I then installed ABarray and its requisite packages. I run the basic analysis for ABarray but consistently run into an error as seen below: > Sys.putenv("R_GSCMD"="/usr/local/bin/gs") > library(ABarray) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. Loading required package: multtest Loading required package: survival Loading required package: splines Welcome to Applied Biosystems AB1700 This package performs analysis for AB1700 gene expression data > eset = ABarray("HFE1rawdata.txt", "hfe1_design.txt", "tissue") Using assayName to match experiment with signal in file: HFE1rawdata.txt The sample names are: [1] "HFE-1" "HFE-2" AssayNames in dataFile: HFE1rawdata.txt [1] "HB00BA6_1/23/07_9:36_AM" "HB00BTX_1/23/07_9:51_AM" Reading data from HFE1rawdata.txt ...... This may take several minutes.... Checking data format:::::::|| The results will be in the folder: Result_tissue/ [1] "Creating plot for Signal Hybridization_Control ..." [1] "Creating plot for Signal Negative_Control ..." [1] "Creating plot for Signal IVT_Kit_Control_BIOB ..." [1] "Creating plot for Signal IVT_Kit_Control_BIOC ..." [1] "Creating plot for Signal IVT_Kit_Control_BIOD ..." [1] "Creating plot for Signal RT_Kit_Control_DAP ..." [1] "Creating plot for Signal RT_Kit_Control_LYS ..." [1] "Creating plot for Signal RT_Kit_Control_PHE ..." Perform basic analysis for non-normalized data ... [1] "Creating barplot for probes detectable ... QC_DetectableProbeSN3" [1] "Creating boxplot for Raw_tissue ..." [1] "Creating correlation matrix and plot Raw_tissue ..." [1] "Creating detection concordance plot Raw_tissue ..." Perform Average imputation for probes with FLAG > 5000 quantile normalized data was saved to: Result_tissue/DataResult/Expression_quantileNormalized.csv The expression data object was saved to R workspace file: hfe1_design_eset_quantile07Feb2007.Rdata Perform data analysis on quantile normalized data ... [1] "Creating boxplot for quantile_tissue ..." [1] "Creating MA plot for quantile_tissue" Error in doPlotEset(esetUse, group, name = normUse, test = test, ...) : could not find function "bmp" > ABarray stops at this point. The documentation makes no mention of "function bmp" or any possible troubleshooting options. My guess is that it is trying to generate .bmp images for the plots immediately prior to the error message but I may be mistaken on that. Googling and searching the mailing list on that assumption revealed a few possible leads, including installing Ghostscript. I have installed Ghostscript and include the "Sys.putenv" command at the beginning of my R sessions to make sure that R is looking for Ghostscript in the correct place. I have a co-worker who has ABarray running correctly on his computer (a Windows box), and while I can use his system to get some of these analyses done quickly, I would much rather be able to run this on my own desktop machine. I am using a Power Mac G5 (PowerPC processors), OS X 10.4.8, R version 2.4.1, BioC 1.9, and Ghostscript 8.54. I have X11 active while using R. Advice of any sort would be greatly appreciated, and again, I hope I have not improperly used the BioConductor list with this request for assistance. Thank you in advance! Alison Ziesel Department of Ophthalmology, Emory University aziesel at emory.edu
abarray • 752 views
ADD COMMENTlink modified 12.7 years ago by James W. MacDonald51k • written 12.7 years ago by Alison Ziesel60
Answer: Problem with ABarray package
0
gravatar for James W. MacDonald
12.7 years ago by
United States
James W. MacDonald51k wrote:
Hi Alison, I took a peek at doPlotEset(), and you are correct; at one point this function is trying to create a bitmap file using the bmp() function (which AFAIK is a Windows only function). The current devel version of ABarray has most of the bmp() calls commented out and replaced by calls to pdf(), although not the one that is giving you problems. As you already noted, you could simply use your co-worker's Windows box to do the analysis. Another alternative would be to write a bmp() function of your own that will cause your ouput to be a pdf instead. Something like (untested!): bmp <- function(filename, width, height){ fn <- paste(pdfDir, sub("\\.bmp$", "\\.pdf", filename), sep="") pdf(file=fn, width=width/100, height=height/100) } You can either write this function in an editor of your choice, save (preferably with a .R extension), and then source() into R before running your code, or just write it in your R session. The benefit of the first case is that you could put it in say your .Rprofile file and have it automatically load any time you start R (either load(myfile.R), or just the function itself). Note that this is sort of a cheesy hack, since we are relying on the assumption that ABarray will create something called 'pdfDir' that we can use within the bmp() function to come up with the correct directory to put the pdf, so this is really an ad hoc fix for this one problem. HTH, Jim Alison Ziesel wrote: > Hello Conductors, > > I have very recently started using R and BioConductor to help with > array analysis for my supervisor and co-workers. I must confess that > I am very much a beginner and I apologize in advance if the question > posed is too basic for this list. > > The first and only BioC package I've been using is ABarray. After > getting R working and running the BiocLite.R install package for > BioConductor, I then installed ABarray and its requisite packages. I > run the basic analysis for ABarray but consistently run into an error > as seen below: > > > > Sys.putenv("R_GSCMD"="/usr/local/bin/gs") > > library(ABarray) > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details > on reading vignettes, see the openVignette help page. > > Loading required package: multtest > Loading required package: survival > Loading required package: splines > > > Welcome to Applied Biosystems AB1700 > This package performs analysis for AB1700 > gene expression data > > eset = ABarray("HFE1rawdata.txt", "hfe1_design.txt", "tissue") > Using assayName to match experiment with signal in file: HFE1rawdata.txt > The sample names are: > [1] "HFE-1" "HFE-2" > AssayNames in dataFile: HFE1rawdata.txt > [1] "HB00BA6_1/23/07_9:36_AM" "HB00BTX_1/23/07_9:51_AM" > Reading data from HFE1rawdata.txt ...... > This may take several minutes.... > Checking data format:::::::|| > > The results will be in the folder: Result_tissue/ > [1] "Creating plot for Signal Hybridization_Control ..." > [1] "Creating plot for Signal Negative_Control ..." > [1] "Creating plot for Signal IVT_Kit_Control_BIOB ..." > [1] "Creating plot for Signal IVT_Kit_Control_BIOC ..." > [1] "Creating plot for Signal IVT_Kit_Control_BIOD ..." > [1] "Creating plot for Signal RT_Kit_Control_DAP ..." > [1] "Creating plot for Signal RT_Kit_Control_LYS ..." > [1] "Creating plot for Signal RT_Kit_Control_PHE ..." > > Perform basic analysis for non-normalized data ... > [1] "Creating barplot for probes detectable ... QC_DetectableProbeSN3" > [1] "Creating boxplot for Raw_tissue ..." > [1] "Creating correlation matrix and plot Raw_tissue ..." > [1] "Creating detection concordance plot Raw_tissue ..." > Perform Average imputation for probes with FLAG > 5000 > > quantile normalized data was saved to: > Result_tissue/DataResult/Expression_quantileNormalized.csv > > The expression data object was saved to R workspace file: > hfe1_design_eset_quantile07Feb2007.Rdata > > Perform data analysis on quantile normalized data ... > [1] "Creating boxplot for quantile_tissue ..." > [1] "Creating MA plot for quantile_tissue" > Error in doPlotEset(esetUse, group, name = normUse, test = test, ...) : > could not find function "bmp" > > > > > ABarray stops at this point. The documentation makes no mention of > "function bmp" or any possible troubleshooting options. My guess is > that it is trying to generate .bmp images for the plots immediately > prior to the error message but I may be mistaken on that. Googling > and searching the mailing list on that assumption revealed a few > possible leads, including installing Ghostscript. I have installed > Ghostscript and include the "Sys.putenv" command at the beginning of > my R sessions to make sure that R is looking for Ghostscript in the > correct place. I have a co-worker who has ABarray running correctly > on his computer (a Windows box), and while I can use his system to > get some of these analyses done quickly, I would much rather be able > to run this on my own desktop machine. > > I am using a Power Mac G5 (PowerPC processors), OS X 10.4.8, R > version 2.4.1, BioC 1.9, and Ghostscript 8.54. I have X11 active > while using R. > > Advice of any sort would be greatly appreciated, and again, I hope I > have not improperly used the BioConductor list with this request for > assistance. Thank you in advance! > > > > Alison Ziesel > Department of Ophthalmology, Emory University > aziesel at emory.edu > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD COMMENTlink written 12.7 years ago by James W. MacDonald51k
Essentially it is because you Mac system cannot make BMP files (the bmp() function does not exists in the CRAN version). Do what James say and ask the maintainer of ABarray to switch to an image format more widely supported. Kasper On Feb 7, 2007, at 9:54 AM, James W. MacDonald wrote: > Hi Alison, > > I took a peek at doPlotEset(), and you are correct; at one point this > function is trying to create a bitmap file using the bmp() function > (which AFAIK is a Windows only function). The current devel version of > ABarray has most of the bmp() calls commented out and replaced by > calls > to pdf(), although not the one that is giving you problems. > > As you already noted, you could simply use your co-worker's Windows > box > to do the analysis. Another alternative would be to write a bmp() > function of your own that will cause your ouput to be a pdf instead. > Something like (untested!): > > bmp <- function(filename, width, height){ > fn <- paste(pdfDir, > sub("\\.bmp$", "\\.pdf", filename), sep="") > pdf(file=fn, width=width/100, height=height/100) > } > > > You can either write this function in an editor of your choice, save > (preferably with a .R extension), and then source() into R before > running your code, or just write it in your R session. The benefit of > the first case is that you could put it in say your .Rprofile file and > have it automatically load any time you start R (either load > (myfile.R), > or just the function itself). > > Note that this is sort of a cheesy hack, since we are relying on the > assumption that ABarray will create something called 'pdfDir' that we > can use within the bmp() function to come up with the correct > directory > to put the pdf, so this is really an ad hoc fix for this one problem. > > HTH, > > Jim > > > > Alison Ziesel wrote: >> Hello Conductors, >> >> I have very recently started using R and BioConductor to help with >> array analysis for my supervisor and co-workers. I must confess that >> I am very much a beginner and I apologize in advance if the question >> posed is too basic for this list. >> >> The first and only BioC package I've been using is ABarray. After >> getting R working and running the BiocLite.R install package for >> BioConductor, I then installed ABarray and its requisite packages. I >> run the basic analysis for ABarray but consistently run into an error >> as seen below: >> >> >>> Sys.putenv("R_GSCMD"="/usr/local/bin/gs") >>> library(ABarray) >> Loading required package: Biobase >> Loading required package: tools >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()' or start with 'help(Biobase)'. For details >> on reading vignettes, see the openVignette help page. >> >> Loading required package: multtest >> Loading required package: survival >> Loading required package: splines >> >> >> Welcome to Applied Biosystems AB1700 >> This package performs analysis for AB1700 >> gene expression data >>> eset = ABarray("HFE1rawdata.txt", "hfe1_design.txt", "tissue") >> Using assayName to match experiment with signal in file: >> HFE1rawdata.txt >> The sample names are: >> [1] "HFE-1" "HFE-2" >> AssayNames in dataFile: HFE1rawdata.txt >> [1] "HB00BA6_1/23/07_9:36_AM" "HB00BTX_1/23/07_9:51_AM" >> Reading data from HFE1rawdata.txt ...... >> This may take several minutes.... >> Checking data format:::::::|| >> >> The results will be in the folder: Result_tissue/ >> [1] "Creating plot for Signal Hybridization_Control ..." >> [1] "Creating plot for Signal Negative_Control ..." >> [1] "Creating plot for Signal IVT_Kit_Control_BIOB ..." >> [1] "Creating plot for Signal IVT_Kit_Control_BIOC ..." >> [1] "Creating plot for Signal IVT_Kit_Control_BIOD ..." >> [1] "Creating plot for Signal RT_Kit_Control_DAP ..." >> [1] "Creating plot for Signal RT_Kit_Control_LYS ..." >> [1] "Creating plot for Signal RT_Kit_Control_PHE ..." >> >> Perform basic analysis for non-normalized data ... >> [1] "Creating barplot for probes detectable ... >> QC_DetectableProbeSN3" >> [1] "Creating boxplot for Raw_tissue ..." >> [1] "Creating correlation matrix and plot Raw_tissue ..." >> [1] "Creating detection concordance plot Raw_tissue ..." >> Perform Average imputation for probes with FLAG > 5000 >> >> quantile normalized data was saved to: >> Result_tissue/DataResult/Expression_quantileNormalized.csv >> >> The expression data object was saved to R workspace file: >> hfe1_design_eset_quantile07Feb2007.Rdata >> >> Perform data analysis on quantile normalized data ... >> [1] "Creating boxplot for quantile_tissue ..." >> [1] "Creating MA plot for quantile_tissue" >> Error in doPlotEset(esetUse, group, name = normUse, test = >> test, ...) : >> could not find function "bmp" >>> >> >> >> ABarray stops at this point. The documentation makes no mention of >> "function bmp" or any possible troubleshooting options. My guess is >> that it is trying to generate .bmp images for the plots immediately >> prior to the error message but I may be mistaken on that. Googling >> and searching the mailing list on that assumption revealed a few >> possible leads, including installing Ghostscript. I have installed >> Ghostscript and include the "Sys.putenv" command at the beginning of >> my R sessions to make sure that R is looking for Ghostscript in the >> correct place. I have a co-worker who has ABarray running correctly >> on his computer (a Windows box), and while I can use his system to >> get some of these analyses done quickly, I would much rather be able >> to run this on my own desktop machine. >> >> I am using a Power Mac G5 (PowerPC processors), OS X 10.4.8, R >> version 2.4.1, BioC 1.9, and Ghostscript 8.54. I have X11 active >> while using R. >> >> Advice of any sort would be greatly appreciated, and again, I hope I >> have not improperly used the BioConductor list with this request for >> assistance. Thank you in advance! >> >> >> >> Alison Ziesel >> Department of Ophthalmology, Emory University >> aziesel at emory.edu >> >> _______________________________________________ >> 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 > > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and > should not be used for urgent or sensitive issues. > > _______________________________________________ > 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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