Problem reading in files with marrayInput
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@richard-friedman-513
Last seen 10.2 years ago
Fellow Expressionists, I am attempting to duplicate the results of Dudoit, Yang, and coworkers on the data of Callow as an exercise for learning to use Spot with my own data. I have tried a subset of six Spot Output files (3 WT, 3KO) as a proof of concept. I am having difficulty reading in the files correctly. I am running marrayInput downloaded on October 30, 2003, R1.8.0, and Windows XP. I would greatly appreciate it if someone could tell me what I am doing incorrectly, suggest something that I can do to debug the procedure, or be willing to look at my input files to see if the problem lies there. Here is a record of my session: ########################################################### > array1.gnames <- read.marrayInfo(file.path(datadir, "array1.gdl"), + info.id =1 labels = 1, skip = 1) Error: syntax error > info.id =1, labels = 1, skip = 1) Error: syntax error > array1.gnames <- read.marrayInfo(file.path(datadir, "array1.gdl"), + info.id =1, labels = 1, skip = 1) > array1.gnames Object of class marrayInfo. maLabels dat[, info.id] 1 2 2 2 3 3 3 4 4 4 5 5 5 6 6 6 7 7 7 8 8 8 9 9 9 10 10 10 11 11 ... Number of labels: 6383 Dimensions of maInfo matrix: 6383 rows by 1 columns Notes: C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.gdl > help.start() updating HTML package listing updating HTML search index If nothing happens, you should open ` C:\PROGRA~1\R\rw1080\doc\html\rwin.html ' yourself > array1.gnames <- read.marrayInfo(file.path(datadir, "array1.gdl"),info.id =6:8, labels = 6, skip = 1) > array1.gnames Object of class marrayInfo. maLabels 1 Cy5RT 2 mSRB1 3 BLANK 4 BLANK 5 BLANK 6 7 5' similar to SW:BTF3_HUMAN P20290 TRANSCRIPTION FACTOR BTF3 ;. gi|1287559|gb|W13502|W13502 [1287559] 8 5' similar to gb:J04794 ALCOHOL DEHYDROGENASE (HUMAN);. gi|1287584|gb|W13547|W13547 [1287584] 9 5'. gi|1287586|gb|W13549|W13549 [1287586] 10 "5' similar to gb:X03747_cds1 SODIUM/POTASSIUM-TRANSPORTING ATPASE BETA-1 (HUMAN); gb:X16646 Mouse mRNA for Na,K-ATPase beta subunit (MOUSE);. gi|1315970|gb|W34060|W34060 [1315970]" Cy3RT 1 Cy5RT 2 mSRB1 3 BLANK 4 BLANK 5 BLANK 6 7 5' similar to SW:BTF3_HUMAN P20290 TRANSCRIPTION FACTOR BTF3 ;. gi|1287559|gb|W13502|W13502 [1287559] 8 5' similar to gb:J04794 ALCOHOL DEHYDROGENASE (HUMAN);. gi|1287584|gb|W13547|W13547 [1287584] 9 5'. gi|1287586|gb|W13549|W13549 [1287586] 10 "5' similar to gb:X03747_cds1 SODIUM/POTASSIUM-TRANSPORTING ATPASE BETA-1 (HUMAN); gb:X16646 Mouse mRNA for Na,K-ATPase beta subunit (MOUSE);. gi|1315970|gb|W34060|W34060 [1315970]" Control BLANK 1 Control BLANK 2 cDNA mSRB1 3 BLANK BLANK 4 BLANK BLANK 5 BLANK BLANK 6 cDNA 317448 7 cDNA 317452 8 cDNA 317456 9 cDNA 317460 10 cDNA 317464 ... Number of labels: 6383 Dimensions of maInfo matrix: 6383 rows by 3 columns Notes: C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.gdl > array1.layout <- read.marrayLayout(fname = file.path(datadir, + "array1.gdl"), ngr =4, ngc = 4, nsr = 19, nsc =21, skip = 1, + ctrl.col =7, id.col = 6) Error in scan(fname, quiet = TRUE, what = h, sep = sep, skip = skip + : unused argument(s) (ctrl.col ...) > array1.layout <- read.marrayLayout(fname = file.path(datadir, + "array1.gdl"), ngr =4, ngc = 4, nsr = 19, nsc =21, skip = 1) > array1.layout Array layout: Object of class marrayLayout. Total number of spots: 6384 Dimensions of grid matrix: 4 rows by 4 cols Dimensions of spot matrices: 19 rows by 21 cols Currently working with a subset of 6384 spots. Control spots: Notes on layout: C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.gdl > arrqy1.samples Error: Object "arrqy1.samples" not found > array1.samples Object of class marrayInfo. maLabels # of slide Names experiment Cy3 experiment Cy5 date comments 1 1 1 array1.1.spot wildtype ref 10/31/2003 NA 2 2 2 array1.2.spot wildtype ref 10/31/2003 NA 3 3 3 array1.3.spot wildtype ref 10/31/2003 NA 4 4 4 array1.4.spot ko ref 10/31/2003 NA 5 5 5 array1.5.spot ko ref 10/31/2003 NA 6 6 6 array1.6.spot ko ref 10/31/2003 NA Number of labels: 6 Dimensions of maInfo matrix: 6 rows by 6 columns Notes: C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1Sample.txt > fnames [1] "array1.1.spot" "array1.2.spot" "array1.3.spot" "array1.4.spot" "array1.5.spot" "array1.6.spot" > array1.raw <- read.marrayRaw(fnames, path = datadir, name.Gf = "Gmean", + name.Gb = "morphG", name.Rf = "Rmean", name.Rb = "morphR", + layout = array1.layout, gnames = array1.gnames, targets = array1.samples) [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.1.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.2.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.3.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.4.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.5.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.6.spot" Warning messages: 1: number of items read is not a multiple of the number of columns 2: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Gf, as.numeric(dat[[name.Gf]])) 3: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Gb, as.numeric(dat[[name.Gb]])) 4: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Rf, as.numeric(dat[[name.Rf]])) 5: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Rb, as.numeric(dat[[name.Rb]])) > ############################################################## Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "Everybody is going to do their book reports on Harry Potter. I'm going to do mine on 'Red Planet'." -Isaac Friedman, age 13 (I know I said "no more Isaac quotes", but I couldn't resist that one).
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@jean-yee-hwa-yang-104
Last seen 10.2 years ago
Hi Richard, Look at the examples in help(read.marrayRaw) Copy and paste the whole set of examples and see if it works. If so, it's possible something is not right with the spot files. Try simply reading the data in: array1.raw <- read.Spot(fnames, path=datadir) and see if it works. Cheers Jean > > array1.raw <- read.marrayRaw(fnames, path = datadir, name.Gf = "Gmean", > + name.Gb = "morphG", name.Rf = "Rmean", name.Rb = "morphR", > + layout = array1.layout, gnames = array1.gnames, targets = > array1.samples) > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.1.spot" > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.2.spot" > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.3.spot" > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.4.spot" write.table(data.frame(AnnA[DEList,],AllData), file=file.path(resdir, "AllData.xls"),sep="\t", row.names=FALSE)> [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.5.spot" > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.6.spot" > Warning messages: > 1: number of items read is not a multiple of the number of columns > 2: number of rows of result > is not a multiple of vector length (arg 2) in: cbind(Gf, > as.numeric(dat[[name.Gf]])) > 3: number of rows of result > is not a multiple of vector length (arg 2) in: cbind(Gb, > as.numeric(dat[[name.Gb]])) > 4: number of rows of result > is not a multiple of vector length (arg 2) in: cbind(Rf, > as.numeric(dat[[name.Rf]])) > 5: number of rows of result > is not a multiple of vector length (arg 2) in: cbind(Rb, > as.numeric(dat[[name.Rb]])) > > > > ############################################################## > Thanks and best wishes, > Rich > ------------------------------------------------------------ > Richard A. Friedman, PhD > Associate Research Scientist > Herbert Irving Comprehensive Cancer Center > Oncoinformatics Core > Lecturer > Department of Biomedical Informatics > Box 95, Room 130BB or P&S 1-420C > Columbia University > 630 W. 168th St. > New York, NY 10032 > (212)305-6901 (5-6901) (voice) > friedman@cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > "Everybody is going to do their book reports on Harry Potter. > I'm going to do mine on 'Red Planet'." -Isaac Friedman, age 13 > (I know I said "no more Isaac quotes", but I couldn't resist that one). > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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On Mon, 3 Nov 2003, Jean Yee Hwa Yang wrote: > Hi Richard, > > Look at the examples in help(read.marrayRaw) > Copy and paste the whole set of examples and see if it works. > If so, it's possible something is not right with the spot files. > > Try simply reading the data in: > array1.raw <- read.Spot(fnames, path=datadir) > and see if it works. > > Cheers > > Jean > Dear Jean and Everybody, Thank you for your reply. I ran the test case in "Introduction to the Bioconductor marrayInput package first, without any error messages. When I ran the session in help(read.marrayRaw) I got the following error messages: ##################################################################### > datadir <- system.file("data", package="marrayInput") > > skip <- grep("Row", readLines(file.path(datadir,"fish.gal"), n=100)) - 1 Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file `C:/PROGRA~1/R/rw1080/library/marrayInput/data/fish.gal' > > swirl.layout <- read.marrayLayout(ngr=4, ngc=4, nsr=22, nsc=24) > > swirl.targets <- read.marrayInfo(file.path(datadir, "SwirlSample.txt")) Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file `C:/PROGRA~1/R/rw1080/library/marrayInput/data/SwirlSample.txt' > > swirl.gnames <- read.marrayInfo(file.path(datadir, "fish.gal"), + info.id=4:5, labels=5, skip=skip) Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file `C:/PROGRA~1/R/rw1080/library/marrayInput/data/fish.gal' > > x <- maInfo(swirl.gnames)[,1] > y <- rep(0, maNspots(swirl.layout)) > y[x == "control"] <- 1 > slot(swirl.layout, "maControls") <- as.factor(y) > > fnames <- dir(path=datadir,pattern=paste("*", "spot", sep="\.")) > swirl<- read.Spot(fnames, path=datadir, + layout = swirl.layout, + gnames = swirl.gnames, + targets = swirl.targets) [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.1.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.2.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.3.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.4.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.5.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.6.spot" Warning messages: 1: number of items read is not a multiple of the number of columns 2: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Gf, as.numeric(dat[[name.Gf]])) 3: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Gb, as.numeric(dat[[name.Gb]])) 4: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Rf, as.numeric(dat[[name.Rf]])) 5: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Rb, as.numeric(dat[[name.Rb]])) Error in read.marrayRaw(fnames = fnames, path = path, name.Gf = name.Gf, : Object "swirl.targets" not found > ###################################################################### #### Two things (at least) are puzzling to me about the above session. 1. I seemed able to read fish.gal when I ran the excercises in the Introduction. fish.gal is in the data directory under the marrayInput directory, in which I am working, Since I opened fish.gal with notepad it appears as a notepad file on the screen. Is that okay? 2. The computer started reading the array1.?.spot files, which the present series of commands had nothing to do. Then I tried reading the spot files the way that you said and their were problems: ###################################################################### #### > fnames <- dir(path=datadir,pattern=paste("*","spot",sep="\.")) > array1.raw <- read.Spot(fnames,path=datadir) [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.1.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.2.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.3.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.4.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.5.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.6.spot" Warning messages: 1: number of items read is not a multiple of the number of columns 2: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Gf, as.numeric(dat[[name.Gf]])) 3: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Gb, as.numeric(dat[[name.Gb]])) 4: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Rf, as.numeric(dat[[name.Rf]])) 5: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Rb, as.numeric(dat[[name.Rb]])) > ################################################################ So clearly there is a problem with the spot files. When I ran summary statistics on array.raw, I got the following: ################################################################# > objects() [1] "array1" "array1.gnames" "array1.layout" "array1.raw" "array1.samples" [6] "ctl" "datadir" "fileIndex" "fnames" "last.warning" [11] "read.marrayInfo" "swirl" "swirl.gnames" "swirl.layout" "swirl.raw" [16] "swirl.samples" "swirl2" "swirl2.gnames" "swirl2.layout" "swirl2.samples" [21] "swirl3" "swirl3..samples" "swirl3.gnames" "swirl3.layout" "swirl3.samples" [26] "x" "y" > array1.raw Pre-normalization intensity data: Object of class marrayRaw. Number of arrays: 6 arrays. A) Layout of spots on the array: Array layout: Object of class marrayLayout. Total number of spots: Dimensions of grid matrix: rows by cols Dimensions of spot matrices: rows by cols Currently working with a subset of spots. Control spots: Notes on layout: B) Samples hybridized to the array: Object of class marrayInfo. NULL data frame with 1 rows Number of labels: 0 Dimensions of maInfo matrix: 0 rows by 0 columns Notes: C) Summary statistics for log-ratio distribution: Min. 1st Qu. Median Mean 3rd Qu. Max NA 1 array1.1.spot -2.16 -0.76 -0.52 -0.44 -0.20 3.50 NA 2 array1.2.spot -2.15 -0.66 -0.44 -0.44 -0.21 2.01 NA 3 array1.3.spot -2.59 -0.84 -0.58 -0.58 -0.31 1.04 NA 4 array1.4.spot -3.46 -0.33 0.09 0.13 0.52 3.53 NA 5 array1.5.spot -3.05 -0.43 -0.15 -0.15 0.12 3.16 NA 6 array1.6.spot -13.08 -0.93 0.29 0.28 2.41 15.43 3664 D) Notes on intensity data: Spot Data > ############################################################### Clearly something is wrong. The files look good to me. May I send you the files (offlist). Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "Everybody is going to do their book reports on Harry Potter. I'm going to do mine on 'Red Planet'." -Isaac Friedman, age 13 (I know I said "no more Isaac quotes", but I couldn't resist that one).
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Dear Jean and Everybody, Please ignore my previous response. The test with the Swirl data works fine. I had put the data in a subdirectory. When I try the second command filesthat you suggested (after moving the swirl.?.spot files out of data ) I get ###################################################################### # > fnames <-dir(path=datadir,pattern=paste("*","spot",sep="\."))[1:6] > array1.raw <- read.Spot(fnames, path=datadir) [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.1.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.2.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.3.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.4.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.5.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.6.spot" Warning messages: 1: number of items read is not a multiple of the number of columns 2: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Gf, as.numeric(dat[[name.Gf]])) 3: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Gb, as.numeric(dat[[name.Gb]])) 4: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Rf, as.numeric(dat[[name.Rf]])) 5: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Rb, as.numeric(dat[[name.Rb]])) > ################################################################## As far as I can see, my array1 spot files are comparable to the swirl files, except that they contain a few extra columns. The last column in the swirl files are badspot. The array1 files have two columns to the right of badspot: nominal.center.row nominal.center.col. Should that make a difference? Thanks and best wishes, Rich On Mon, 3 Nov 2003, Jean Yee Hwa Yang wrote: > Hi Richard, > > Look at the examples in help(read.marrayRaw) > Copy and paste the whole set of examples and see if it works. > If so, it's possible something is not right with the spot files. > > Try simply reading the data in: > array1.raw <- read.Spot(fnames, path=datadir) > and see if it works. > > Cheers > > Jean > > > > array1.raw <- read.marrayRaw(fnames, path = datadir, name.Gf = "Gmean", > > + name.Gb = "morphG", name.Rf = "Rmean", name.Rb = "morphR", > > + layout = array1.layout, gnames = array1.gnames, targets = > > array1.samples) > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.1.spot" > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.2.spot" > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.3.spot" > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.4.spot" > write.table(data.frame(AnnA[DEList,],AllData), file=file.path(resdir, > "AllData.xls"),sep="\t", row.names=FALSE)> > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.5.spot" > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.6.spot" > > Warning messages: > > 1: number of items read is not a multiple of the number of columns > > 2: number of rows of result > > is not a multiple of vector length (arg 2) in: cbind(Gf, > > as.numeric(dat[[name.Gf]])) > > 3: number of rows of result > > is not a multiple of vector length (arg 2) in: cbind(Gb, > > as.numeric(dat[[name.Gb]])) > > 4: number of rows of result > > is not a multiple of vector length (arg 2) in: cbind(Rf, > > as.numeric(dat[[name.Rf]])) > > 5: number of rows of result > > is not a multiple of vector length (arg 2) in: cbind(Rb, > > as.numeric(dat[[name.Rb]])) > > > > > > > ############################################################## > > Thanks and best wishes, > > Rich > > ------------------------------------------------------------ > > Richard A. Friedman, PhD > > Associate Research Scientist > > Herbert Irving Comprehensive Cancer Center > > Oncoinformatics Core > > Lecturer > > Department of Biomedical Informatics > > Box 95, Room 130BB or P&S 1-420C > > Columbia University > > 630 W. 168th St. > > New York, NY 10032 > > (212)305-6901 (5-6901) (voice) > > friedman@cancercenter.columbia.edu > > http://cancercenter.columbia.edu/~friedman/ > > > > "Everybody is going to do their book reports on Harry Potter. > > I'm going to do mine on 'Red Planet'." -Isaac Friedman, age 13 > > (I know I said "no more Isaac quotes", but I couldn't resist that one). > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "In slumberland there are 100 kinds of halavah and you have to eat every one." -Rose Friedman, age 7
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Hi Richard, Could you place array1.5.spot and array1.6.spot online somewhere for me to download or e-mail the two files for me to take a look. Cheers Jean > #################################################################### ### > > fnames <-dir(path=datadir,pattern=paste("*","spot",sep="\."))[1:6] > > array1.raw <- read.Spot(fnames, path=datadir) > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.1.spot" > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.2.spot" > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.3.spot" > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.4.spot" > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.5.spot" > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.6.spot" > Warning messages: > 1: number of items read is not a multiple of the number of columns > 2: number of rows of result > is not a multiple of vector length (arg 2) in: cbind(Gf, > as.numeric(dat[[name.Gf]])) > 3: number of rows of result > is not a multiple of vector length (arg 2) in: cbind(Gb, > as.numeric(dat[[name.Gb]])) > 4: number of rows of result > is not a multiple of vector length (arg 2) in: cbind(Rf, > as.numeric(dat[[name.Rf]])) > 5: number of rows of result > is not a multiple of vector length (arg 2) in: cbind(Rb, > as.numeric(dat[[name.Rb]])) > > > ################################################################## > As far as I can see, my array1 spot files are comparable to the > swirl files, except that they contain a few extra columns. > The last column in the swirl files are badspot. The array1 files have > two columns to the right of badspot: nominal.center.row > nominal.center.col. Should that make a difference? > > Thanks and best wishes, > Rich > > On Mon, 3 Nov 2003, Jean Yee Hwa Yang wrote: > > > Hi Richard, > > > > Look at the examples in help(read.marrayRaw) > > Copy and paste the whole set of examples and see if it works. > > If so, it's possible something is not right with the spot files. > > > > Try simply reading the data in: > > array1.raw <- read.Spot(fnames, path=datadir) > > and see if it works. > > > > Cheers > > > > Jean > > > > > > array1.raw <- read.marrayRaw(fnames, path = datadir, name.Gf = "Gmean", > > > + name.Gb = "morphG", name.Rf = "Rmean", name.Rb = "morphR", > > > + layout = array1.layout, gnames = array1.gnames, targets = > > > array1.samples) > > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.1.spot" > > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.2.spot" > > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.3.spot" > > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.4.spot" > > write.table(data.frame(AnnA[DEList,],AllData), file=file.path(resdir, > > "AllData.xls"),sep="\t", row.names=FALSE)> > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.5.spot" > > > [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.6.spot" > > > Warning messages: > > > 1: number of items read is not a multiple of the number of columns > > > 2: number of rows of result > > > is not a multiple of vector length (arg 2) in: cbind(Gf, > > > as.numeric(dat[[name.Gf]])) > > > 3: number of rows of result > > > is not a multiple of vector length (arg 2) in: cbind(Gb, > > > as.numeric(dat[[name.Gb]])) > > > 4: number of rows of result > > > is not a multiple of vector length (arg 2) in: cbind(Rf, > > > as.numeric(dat[[name.Rf]])) > > > 5: number of rows of result > > > is not a multiple of vector length (arg 2) in: cbind(Rb, > > > as.numeric(dat[[name.Rb]])) > > > > > > > > > > ############################################################## > > > Thanks and best wishes, > > > Rich > > > ------------------------------------------------------------ > > > Richard A. Friedman, PhD > > > Associate Research Scientist > > > Herbert Irving Comprehensive Cancer Center > > > Oncoinformatics Core > > > Lecturer > > > Department of Biomedical Informatics > > > Box 95, Room 130BB or P&S 1-420C > > > Columbia University > > > 630 W. 168th St. > > > New York, NY 10032 > > > (212)305-6901 (5-6901) (voice) > > > friedman@cancercenter.columbia.edu > > > http://cancercenter.columbia.edu/~friedman/ > > > > > > "Everybody is going to do their book reports on Harry Potter. > > > I'm going to do mine on 'Red Planet'." -Isaac Friedman, age 13 > > > (I know I said "no more Isaac quotes", but I couldn't resist that one). > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > > ------------------------------------------------------------ > Richard A. Friedman, PhD > Associate Research Scientist > Herbert Irving Comprehensive Cancer Center > Oncoinformatics Core > Lecturer > Department of Biomedical Informatics > Box 95, Room 130BB or P&S 1-420C > Columbia University > 630 W. 168th St. > New York, NY 10032 > (212)305-6901 (5-6901) (voice) > friedman@cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > "In slumberland there are 100 kinds of halavah and you > have to eat every one." -Rose Friedman, age 7 >
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@james-w-macdonald-5106
Last seen 10 hours ago
United States
I think your error is in the first line of your example. You are missing a comma between info.id=1 and labels=1. Any time you see 'Error: syntax error', you should look at the preceding line to see where the error lies. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Richard Friedman <friedman@cancercenter.columbia.edu> 11/03/03 05:21PM >>> Fellow Expressionists, I am attempting to duplicate the results of Dudoit, Yang, and coworkers on the data of Callow as an exercise for learning to use Spot with my own data. I have tried a subset of six Spot Output files (3 WT, 3KO) as a proof of concept. I am having difficulty reading in the files correctly. I am running marrayInput downloaded on October 30, 2003, R1.8.0, and Windows XP. I would greatly appreciate it if someone could tell me what I am doing incorrectly, suggest something that I can do to debug the procedure, or be willing to look at my input files to see if the problem lies there. Here is a record of my session: ########################################################### > array1.gnames <- read.marrayInfo(file.path(datadir, "array1.gdl"), + info.id =1 labels = 1, skip = 1) Error: syntax error > info.id =1, labels = 1, skip = 1) Error: syntax error > array1.gnames <- read.marrayInfo(file.path(datadir, "array1.gdl"), + info.id =1, labels = 1, skip = 1) > array1.gnames Object of class marrayInfo. maLabels dat[, info.id] 1 2 2 2 3 3 3 4 4 4 5 5 5 6 6 6 7 7 7 8 8 8 9 9 9 10 10 10 11 11 ... Number of labels: 6383 Dimensions of maInfo matrix: 6383 rows by 1 columns Notes: C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.gdl > help.start() updating HTML package listing updating HTML search index If nothing happens, you should open ` C:\PROGRA~1\R\rw1080\doc\html\rwin.html ' yourself > array1.gnames <- read.marrayInfo(file.path(datadir, "array1.gdl"),info.id =6:8, labels = 6, skip = 1) > array1.gnames Object of class marrayInfo. maLabels 1 Cy5RT 2 mSRB1 3 BLANK 4 BLANK 5 BLANK 6 7 5' similar to SW:BTF3_HUMAN P20290 TRANSCRIPTION FACTOR BTF3 ;. gi|1287559|gb|W13502|W13502 [1287559] 8 5' similar to gb:J04794 ALCOHOL DEHYDROGENASE (HUMAN);. gi|1287584|gb|W13547|W13547 [1287584] 9 5'. gi|1287586|gb|W13549|W13549 [1287586] 10 "5' similar to gb:X03747_cds1 SODIUM/POTASSIUM-TRANSPORTING ATPASE BETA-1 (HUMAN); gb:X16646 Mouse mRNA for Na,K-ATPase beta subunit (MOUSE);. gi|1315970|gb|W34060|W34060 [1315970]" Cy3RT 1 Cy5RT 2 mSRB1 3 BLANK 4 BLANK 5 BLANK 6 7 5' similar to SW:BTF3_HUMAN P20290 TRANSCRIPTION FACTOR BTF3 ;. gi|1287559|gb|W13502|W13502 [1287559] 8 5' similar to gb:J04794 ALCOHOL DEHYDROGENASE (HUMAN);. gi|1287584|gb|W13547|W13547 [1287584] 9 5'. gi|1287586|gb|W13549|W13549 [1287586] 10 "5' similar to gb:X03747_cds1 SODIUM/POTASSIUM-TRANSPORTING ATPASE BETA-1 (HUMAN); gb:X16646 Mouse mRNA for Na,K-ATPase beta subunit (MOUSE);. gi|1315970|gb|W34060|W34060 [1315970]" Control BLANK 1 Control BLANK 2 cDNA mSRB1 3 BLANK BLANK 4 BLANK BLANK 5 BLANK BLANK 6 cDNA 317448 7 cDNA 317452 8 cDNA 317456 9 cDNA 317460 10 cDNA 317464 ... Number of labels: 6383 Dimensions of maInfo matrix: 6383 rows by 3 columns Notes: C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.gdl > array1.layout <- read.marrayLayout(fname = file.path(datadir, + "array1.gdl"), ngr =4, ngc = 4, nsr = 19, nsc =21, skip = 1, + ctrl.col =7, id.col = 6) Error in scan(fname, quiet = TRUE, what = h, sep = sep, skip = skip + : unused argument(s) (ctrl.col ...) > array1.layout <- read.marrayLayout(fname = file.path(datadir, + "array1.gdl"), ngr =4, ngc = 4, nsr = 19, nsc =21, skip = 1) > array1.layout Array layout: Object of class marrayLayout. Total number of spots: 6384 Dimensions of grid matrix: 4 rows by 4 cols Dimensions of spot matrices: 19 rows by 21 cols Currently working with a subset of 6384 spots. Control spots: Notes on layout: C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.gdl > arrqy1.samples Error: Object "arrqy1.samples" not found > array1.samples Object of class marrayInfo. maLabels # of slide Names experiment Cy3 experiment Cy5 date comments 1 1 1 array1.1.spot wildtype ref 10/31/2003 NA 2 2 2 array1.2.spot wildtype ref 10/31/2003 NA 3 3 3 array1.3.spot wildtype ref 10/31/2003 NA 4 4 4 array1.4.spot ko ref 10/31/2003 NA 5 5 5 array1.5.spot ko ref 10/31/2003 NA 6 6 6 array1.6.spot ko ref 10/31/2003 NA Number of labels: 6 Dimensions of maInfo matrix: 6 rows by 6 columns Notes: C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1Sample.txt > fnames [1] "array1.1.spot" "array1.2.spot" "array1.3.spot" "array1.4.spot" "array1.5.spot" "array1.6.spot" > array1.raw <- read.marrayRaw(fnames, path = datadir, name.Gf = "Gmean", + name.Gb = "morphG", name.Rf = "Rmean", name.Rb = "morphR", + layout = array1.layout, gnames = array1.gnames, targets = array1.samples) [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.1.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.2.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.3.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.4.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.5.spot" [1] "Reading C:/PROGRA~1/R/rw1080/library/marrayInput/data/array1.6.spot" Warning messages: 1: number of items read is not a multiple of the number of columns 2: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Gf, as.numeric(dat[[name.Gf]])) 3: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Gb, as.numeric(dat[[name.Gb]])) 4: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Rf, as.numeric(dat[[name.Rf]])) 5: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Rb, as.numeric(dat[[name.Rb]])) > ############################################################## Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "Everybody is going to do their book reports on Harry Potter. I'm going to do mine on 'Red Planet'." -Isaac Friedman, age 13 (I know I said "no more Isaac quotes", but I couldn't resist that one). _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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