question about read.marrayRaw
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Ren Na ▴ 250
@ren-na-870
Last seen 10.2 years ago
I try to create a marrayRaw object. The problem I am having is that only the first line of my every .spot file has been read by the function read.marrayRaw. The following is what I did, xpd.layout <- read.marrayLayout(fname="Mouse24052004.txt", ngr=8, ngc=4, nsr=23, nsc=23, skip=0, ctl.col=6) xpd.samples<- read.marrayInfo("sample.txt") xpd.gnames<-read.marrayInfo("Mouse24052004.txt", info.id=6, labels=10, skip=0) targets <- readTargets("Targets.txt") fnames<-targets$FileName xpd.raw<-read.marrayRaw(fnames, name.Gf="Gmedian", name.Gb="morphG", name.Rf="Rmedian", name.Rb="morphR", layout=xpd.layout, gnames=xpd.gnames, targets=xpd.samples) > xpd.raw An object of class "marrayRaw" @maRf ./1391.spot ./1392.spot ./1348.spot ./1349.spot ./1373.spot ./1374.spot [1,] 621 217 639 539 329 290 ./1393.spot ./1394.spot ./1358.spot ./1359.spot ./1371.spot ./1372.spot [1,] 1704 198 606 563 562 1052 ./1387.spot ./1388.spot ./1397.spot ./1398.spot ./1399.spot ./1390.spot [1,] 817 101 297 433 1926 650 @maGf ./1391.spot ./1392.spot ./1348.spot ./1349.spot ./1373.spot ./1374.spot [1,] 380 657 555 554 638 346 ./1393.spot ./1394.spot ./1358.spot ./1359.spot ./1371.spot ./1372.spot [1,] 3267 349 503 635 844 1596 ./1387.spot ./1388.spot ./1397.spot ./1398.spot ./1399.spot ./1390.spot [1,] 1078 90 334 549 2118 1093 @maRb ...................................................................... ......... ...................................................................... ......... I couldn't figure out what I did wrong. Thanks for any help. Ren
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@gustavo-henrique-esteves-937
Last seen 9.4 years ago
Brazil
Hello Ren, Try to set the maSub in your marrayLayout object to a vector of TRUEs with length equal to the number of spots you have in your files. I have had the same problem and doing this resolved to me. Well hapened to me in R-1.9.1 with the last marray package. In the previous versions I didn't have this problem. What version of R / marray are you using? Gustavo On Fri, 01 Oct 2004 16:46:03 -0500, Ren Na <na@uthscsa.edu> wrote: > I try to create a marrayRaw object. The problem I am having is that only > the first line of my every .spot file has been read by the function > read.marrayRaw. The following is what I did, > xpd.layout <- read.marrayLayout(fname="Mouse24052004.txt", ngr=8, ngc=4, > nsr=23, nsc=23, skip=0, ctl.col=6) > xpd.samples<- read.marrayInfo("sample.txt") > xpd.gnames<-read.marrayInfo("Mouse24052004.txt", info.id=6, labels=10, > skip=0) > targets <- readTargets("Targets.txt") > fnames<-targets$FileName > xpd.raw<-read.marrayRaw(fnames, name.Gf="Gmedian", name.Gb="morphG", > name.Rf="Rmedian", name.Rb="morphR", layout=xpd.layout, > gnames=xpd.gnames, targets=xpd.samples) > > xpd.raw > An object of class "marrayRaw" > @maRf > ./1391.spot ./1392.spot ./1348.spot ./1349.spot ./1373.spot ./1374.spot > [1,] 621 217 639 539 329 290 > ./1393.spot ./1394.spot ./1358.spot ./1359.spot ./1371.spot ./1372.spot > [1,] 1704 198 606 563 562 1052 > ./1387.spot ./1388.spot ./1397.spot ./1398.spot ./1399.spot ./1390.spot > [1,] 817 101 297 433 1926 650 > > @maGf > ./1391.spot ./1392.spot ./1348.spot ./1349.spot ./1373.spot ./1374.spot > [1,] 380 657 555 554 638 346 > ./1393.spot ./1394.spot ./1358.spot ./1359.spot ./1371.spot ./1372.spot > [1,] 3267 349 503 635 844 1596 > ./1387.spot ./1388.spot ./1397.spot ./1398.spot ./1399.spot ./1390.spot > [1,] 1078 90 334 549 2118 1093 > > @maRb > .................................................................... ........... > .................................................................... ........... > I couldn't figure out what I did wrong. Thanks for any help. > > Ren > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- _______________________________________________________________ "The truth you speak has no past and no future. It is, and that's all it needs to be." "A verdade que voc? fala n?o tem passado nem futuro. Ela ?, e isso ? tudo que ela precisa ser." Autor desconhecido _______________________________________________________________ Gustavo Henrique Esteves e-mail: gesteves@gmail.com Home Page: http://www.vision.ime.usp.br/~gesteves/
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Gustavo Henrique Esteves wrote: >Hello Ren, > >Try to set the maSub in your marrayLayout object to a vector of TRUEs >with length equal to the number of spots you have in your files. I >have had the same problem and doing this resolved to me. > >Well hapened to me in R-1.9.1 with the last marray package. In the >previous versions I didn't have this problem. What version of R / >marray are you using? > >Gustavo > > > > >On Fri, 01 Oct 2004 16:46:03 -0500, Ren Na <na@uthscsa.edu> wrote: > > >>I try to create a marrayRaw object. The problem I am having is that only >>the first line of my every .spot file has been read by the function >>read.marrayRaw. The following is what I did, >>xpd.layout <- read.marrayLayout(fname="Mouse24052004.txt", ngr=8, ngc=4, >>nsr=23, nsc=23, skip=0, ctl.col=6) >>xpd.samples<- read.marrayInfo("sample.txt") >>xpd.gnames<-read.marrayInfo("Mouse24052004.txt", info.id=6, labels=10, >>skip=0) >>targets <- readTargets("Targets.txt") >>fnames<-targets$FileName >>xpd.raw<-read.marrayRaw(fnames, name.Gf="Gmedian", name.Gb="morphG", >>name.Rf="Rmedian", name.Rb="morphR", layout=xpd.layout, >>gnames=xpd.gnames, targets=xpd.samples) >> > xpd.raw >>An object of class "marrayRaw" >>@maRf >> ./1391.spot ./1392.spot ./1348.spot ./1349.spot ./1373.spot ./1374.spot >>[1,] 621 217 639 539 329 290 >> ./1393.spot ./1394.spot ./1358.spot ./1359.spot ./1371.spot ./1372.spot >>[1,] 1704 198 606 563 562 1052 >> ./1387.spot ./1388.spot ./1397.spot ./1398.spot ./1399.spot ./1390.spot >>[1,] 817 101 297 433 1926 650 >> >>@maGf >> ./1391.spot ./1392.spot ./1348.spot ./1349.spot ./1373.spot ./1374.spot >>[1,] 380 657 555 554 638 346 >> ./1393.spot ./1394.spot ./1358.spot ./1359.spot ./1371.spot ./1372.spot >>[1,] 3267 349 503 635 844 1596 >> ./1387.spot ./1388.spot ./1397.spot ./1398.spot ./1399.spot ./1390.spot >>[1,] 1078 90 334 549 2118 1093 >> >>@maRb >>.................................................................... ........... >>.................................................................... ........... >>I couldn't figure out what I did wrong. Thanks for any help. >> >>Ren >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> > > > > > Hi, Gustavo, Thank you very much, it works with your suggestion. I had exactly same experience like you. I am using R(1.9.1) and the last marray package(1.5.14). And I didn't have this problem before. Ren
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Marcus Davy ▴ 680
@marcus-davy-374
Last seen 10.2 years ago
Hi, the reason for the problem is due to a slight bug in the package 'marray', specifically in the function read.marrayRaw. > packageDescription("marray", fields="Version") [1] "1.5.14" The function read.marrayRaw in 'marray' uses read.table whereas the function version of read.marrayRaw in 'marrayInput' uses scan to upload the data. Reproducing the problem using the example from the marray vignette example: library(marray) datadir <- system.file("swirldata", package = "marray") dir(datadir) swirl.layout <- read.marrayLayout(fname = file.path(datadir,"fish.gal"), ngr = 4, ngc = 4, nsr = 22, nsc = 24, skip = 21, ctl.col = 4) ctl <- rep("Control", maNspots(swirl.layout)) ctl[maControls(swirl.layout) != "control"] <- "N" maControls(swirl.layout) <- factor(ctl) swirl.layout swirl.samples <- read.marrayInfo(file.path(datadir, "SwirlSample.txt")) swirl.gnames <- read.marrayInfo(file.path(datadir, "fish.gal"), info.id = 4:5, labels = 5, skip = 21) fnames <- dir(path = datadir, pattern = paste("*", "spot", sep = ".")) swirl.raw <- read.marrayRaw(fnames, path = datadir, name.Gf = "Gmean", name.Gb = "morphG", name.Rf = "Rmean", name.Rb = "morphR", layout = swirl.layout, gnames = swirl.gnames, targets = swirl.samples) maRf(swirl.raw) /usr/local/lib/R/library/marray/swirldata/swirl.1.spot [1,] 19538.47 /usr/local/lib/R/library/marray/swirldata/swirl.2.spot [1,] 16138.72 /usr/local/lib/R/library/marray/swirldata/swirl.3.spot [1,] 2895.16 /usr/local/lib/R/library/marray/swirldata/swirl.4.spot [1,] 14054.54 Only the first line of each spot file has been loaded in using read.marrayRaw. When the swirl.layout object is defined, the slot maSub is TRUE of length 1, > maSub(swirl.layout) [1] TRUE In read.marrayRaw, read.table uses this slot to define the number of spots for nrows, which is the number of rows to read in. Inside read.marrayRaw... nspots <- sum(layout@maSub) # of length 1 ... dat <- read.table(f, skip = skip2, header = TRUE, sep = sep, as.is = TRUE, quote = quote, check.names = FALSE, comment.char = "", nrows = nspots, ...) # data of length 1 Quick work around is to define the layout *after* reading in the data. library(marray) datadir <- system.file("swirldata", package = "marray") dir(datadir) swirl.samples <- read.marrayInfo(file.path(datadir, "SwirlSample.txt")) swirl.gnames <- read.marrayInfo(file.path(datadir, "fish.gal"), info.id = 4:5, labels = 5, skip = 21) fnames <- dir(path = datadir, pattern = paste("*", "spot", sep = ".")) swirl.raw <- read.marrayRaw(fnames, path = datadir, name.Gf = "Gmean", name.Gb = "morphG", name.Rf = "Rmean", name.Rb = "morphR", gnames = swirl.gnames, targets = swirl.samples) swirl.layout <- read.marrayLayout(fname = file.path(datadir,"fish.gal"), ngr = 4, ngc = 4, nsr = 22, nsc = 24, skip = 21, ctl.col = 4) ctl <- rep("Control", maNspots(swirl.layout)) ctl[maControls(swirl.layout) != "control"] <- "N" maControls(swirl.layout) <- factor(ctl) swirl.layout maLayout(swirl.raw) <- swirl.layout dim(maRf(swirl.raw)) [1] 8448 4 Now all the data is uploaded. marcus >>> Ren Na <na@uthscsa.edu> 5/10/2004 3:51:09 AM >>> Gustavo Henrique Esteves wrote: >Hello Ren, > >Try to set the maSub in your marrayLayout object to a vector of TRUEs >with length equal to the number of spots you have in your files. I >have had the same problem and doing this resolved to me. > >Well hapened to me in R-1.9.1 with the last marray package. In the >previous versions I didn't have this problem. What version of R / >marray are you using? > >Gustavo > > > > >On Fri, 01 Oct 2004 16:46:03 -0500, Ren Na <na@uthscsa.edu> wrote: > > >>I try to create a marrayRaw object. The problem I am having is that only >>the first line of my every .spot file has been read by the function >>read.marrayRaw. The following is what I did, >>xpd.layout <- read.marrayLayout(fname="Mouse24052004.txt", ngr=8, ngc=4, >>nsr=23, nsc=23, skip=0, ctl.col=6) >>xpd.samples<- read.marrayInfo("sample.txt") >>xpd.gnames<-read.marrayInfo("Mouse24052004.txt", info.id=6, labels=10, >>skip=0) >>targets <- readTargets("Targets.txt") >>fnames<-targets$FileName >>xpd.raw<-read.marrayRaw(fnames, name.Gf="Gmedian", name.Gb="morphG", >>name.Rf="Rmedian", name.Rb="morphR", layout=xpd.layout, >>gnames=xpd.gnames, targets=xpd.samples) >> > xpd.raw >>An object of class "marrayRaw" >>@maRf >> ./1391.spot ./1392.spot ./1348.spot ./1349.spot ./1373.spot ./1374.spot >>[1,] 621 217 639 539 329 290 >> ./1393.spot ./1394.spot ./1358.spot ./1359.spot ./1371.spot ./1372.spot >>[1,] 1704 198 606 563 562 1052 >> ./1387.spot ./1388.spot ./1397.spot ./1398.spot ./1399.spot ./1390.spot >>[1,] 817 101 297 433 1926 650 >> >>@maGf >> ./1391.spot ./1392.spot ./1348.spot ./1349.spot ./1373.spot ./1374.spot >>[1,] 380 657 555 554 638 346 >> ./1393.spot ./1394.spot ./1358.spot ./1359.spot ./1371.spot ./1372.spot >>[1,] 3267 349 503 635 844 1596 >> ./1387.spot ./1388.spot ./1397.spot ./1398.spot ./1399.spot ./1390.spot >>[1,] 1078 90 334 549 2118 1093 >> >>@maRb >>.................................................................... ........... >>.................................................................... ........... >>I couldn't figure out what I did wrong. Thanks for any help. >> >>Ren >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> > > > > > Hi, Gustavo, Thank you very much, it works with your suggestion. I had exactly same experience like you. I am using R(1.9.1) and the last marray package(1.5.14). And I didn't have this problem before. Ren _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}
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