Problems loading mraw
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Amy Mikhail ▴ 460
@amy-mikhail-1317
Last seen 9.6 years ago
Dear all, I am new to R and currently trying to follow some vignettes, swapping the example files for my own data. I am using R 2.1.0, Bioconductor I have downloaded from a CD provided at the (recent) microarray analysis course in Bressanone, Italy. I've been trying to work through various parts of the following vignettes: (a) "Quick start guide for marray" (b) "Introduction to the Bioconductor marray package: Input component" So far I can import and read my files ok, but have had problems with the the following: > maQualityPlots(mraw) I was originally getting a "colorspace not found" error message similar to that of Naomi's post, so I downloaded the package from the website that was indicated in one of her replies. But now I'm getting a new error message: > maQualityPlots(mraw) Loading required package: hexbin Loading required package: grid Loading required package: colorspace Attaching package: 'colorspace' The following object(s) are masked from package:grDevices : hcl Error in inherits(x, "factor") : Object "mraw" not found Does this mean there is something else I should download? Would you suggest I download all of bioconductor again, or just look for that particular passage? On a separate note, I did manage to create an image of my data but am having a bit of trouble working out which slide it is coming from; I have read in two .gpr files, "TAMnoamp.gpr" and "TAMwithamp.gpr": > library("marray") > dir(system.file("mossiedata",package="marray")) [1] "MMC2_grid.gal" "mossieData.txt" "TAMnoamp.gpr" "TAMwithamp.gpr" > datadir<-system.file("mossiedata",package="marray") > setwd(datadir) > mossiedataTargets<-read.marrayInfo(file.path(datadir,"mossieData.txt ")) > data<-read.GenePix(fnames="TAMnoamp.gpr") Reading ... TAMnoamp.gpr > data<-read.GenePix(fnames="TAMwithamp.gpr") Reading ... TAMwithamp.gpr > mossiedata.gnames<-read.marrayInfo(file.path(datadir,"MMC2_grid.gal"), + info.id=4:5,labels=5,skip=30) > summary(mossiedata.gnames) Object of class marrayInfo. maLabels Name ID 1 Cal. 01 cYIR01 Cal. 01 2 Cal. 04 cYIR04 Cal. 04 3 Cal. 07 cYIR07 Cal. 07 4 Cal. 10 cYIR10 Cal. 10 5 Cal. 01 cYIR01 Cal. 01 6 Cal. 04 cYIR04 Cal. 04 7 Cal. 07 cYIR07 Cal. 07 8 Cal. 10 cYIR10 Cal. 10 9 Cal. 03 cYIR03 Cal. 03 10 Cal. 05 cYIR05 Cal. 05 ... Number of labels: 13440 Dimensions of maInfo matrix: 13440 rows by 2 columns Notes: C:/PROGRA~1/R/rw2010/library/marray/mossiedata/MMC2_grid.gal > library(arrayQuality) Loading required package: convert Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. [1] "arrayQuality" [1] "Checking for missing packages" Garbage collection 135 = 74+19+42 (level 2) ... 809344 cons cells free (67%) 15.1 Mbytes of heap free (78%) [1] "Loading required packages" Attaching package: 'mclust' The following object(s) are masked from package:stats : density > image(data) [1] FALSE NULL Does this mean that the image I get is from the second file only (TAMwithamp.gpr) since that is the last one assigned to "data"? Is there any way of writing titles on the graphs / objects (with this code all that is written on the top of the image is ":image of M")? Also what does "masked from package stats" mean? Appologies for writing such a long post and asking so many questions... Looking forward to any replies and suggestions, Amy. ------------------------------------------- Amy Mikhail Research student University of Aberdeen Zoology Building Tillydrone Avenue Aberdeen AB24 2TZ Scotland Email: a.mikhail at abdn.ac.uk Phone: 00-44-1224-272880 (lab)
Microarray marray Microarray marray • 1.2k views
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Paquet, Agnes ▴ 500
@paquet-agnes-807
Last seen 9.6 years ago
Hi Amy, I haven't looked at the vignette you are using, so I will try to answer your questions in a general way. The error message " Error in inherits(x, "factor") : Object "mraw" not found" means that the object "mraw" does not exist in your working environment. You can check what objects are in your environment using the command ls(). maQualityPlots takes as argument a marrayRaw or marrayNorm object created for example using read.GenePix. In your case, you will need to do something like: mraw <- read.GenePix(fnames="TAMwithamp.gpr") maQualityPlots(mraw) This command will only read the file names TAMwithamp.gpr. If you want to read in all gpr files that are in your working directory, you can for example either not specify any file names: mraw <- read.GenePix() or specify all files names: mraw <- read.GenePix(fnames=c("TAMnoamp.gpr", " TAMwithamp.gpr")) "masked from package stats" means that the function "density" from package "stats" is overwriting the "density" function in package "mclust". It shouldn't be any problem here. I hope this will help. If you have any other questions about maQualityPlots, please let me know. Regards, Agnes -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Amy Mikhail Sent: Monday, July 25, 2005 12:40 PM To: bioconductor at stat.math.ethz.ch Subject: [BioC] Problems loading mraw Dear all, I am new to R and currently trying to follow some vignettes, swapping the example files for my own data. I am using R 2.1.0, Bioconductor I have downloaded from a CD provided at the (recent) microarray analysis course in Bressanone, Italy. I've been trying to work through various parts of the following vignettes: (a) "Quick start guide for marray" (b) "Introduction to the Bioconductor marray package: Input component" So far I can import and read my files ok, but have had problems with the the following: > maQualityPlots(mraw) I was originally getting a "colorspace not found" error message similar to that of Naomi's post, so I downloaded the package from the website that was indicated in one of her replies. But now I'm getting a new error message: > maQualityPlots(mraw) Loading required package: hexbin Loading required package: grid Loading required package: colorspace Attaching package: 'colorspace' The following object(s) are masked from package:grDevices : hcl Error in inherits(x, "factor") : Object "mraw" not found Does this mean there is something else I should download? Would you suggest I download all of bioconductor again, or just look for that particular passage? On a separate note, I did manage to create an image of my data but am having a bit of trouble working out which slide it is coming from; I have read in two .gpr files, "TAMnoamp.gpr" and "TAMwithamp.gpr": > library("marray") > dir(system.file("mossiedata",package="marray")) [1] "MMC2_grid.gal" "mossieData.txt" "TAMnoamp.gpr" "TAMwithamp.gpr" > datadir<-system.file("mossiedata",package="marray") > setwd(datadir) > mossiedataTargets<-read.marrayInfo(file.path(datadir,"mossieData.txt") ) > data<-read.GenePix(fnames="TAMnoamp.gpr") Reading ... TAMnoamp.gpr > data<-read.GenePix(fnames="TAMwithamp.gpr") Reading ... TAMwithamp.gpr > mossiedata.gnames<-read.marrayInfo(file.path(datadir,"MMC2_grid.gal"), + info.id=4:5,labels=5,skip=30) > summary(mossiedata.gnames) Object of class marrayInfo. maLabels Name ID 1 Cal. 01 cYIR01 Cal. 01 2 Cal. 04 cYIR04 Cal. 04 3 Cal. 07 cYIR07 Cal. 07 4 Cal. 10 cYIR10 Cal. 10 5 Cal. 01 cYIR01 Cal. 01 6 Cal. 04 cYIR04 Cal. 04 7 Cal. 07 cYIR07 Cal. 07 8 Cal. 10 cYIR10 Cal. 10 9 Cal. 03 cYIR03 Cal. 03 10 Cal. 05 cYIR05 Cal. 05 ... Number of labels: 13440 Dimensions of maInfo matrix: 13440 rows by 2 columns Notes: C:/PROGRA~1/R/rw2010/library/marray/mossiedata/MMC2_grid.gal > library(arrayQuality) Loading required package: convert Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. [1] "arrayQuality" [1] "Checking for missing packages" Garbage collection 135 = 74+19+42 (level 2) ... 809344 cons cells free (67%) 15.1 Mbytes of heap free (78%) [1] "Loading required packages" Attaching package: 'mclust' The following object(s) are masked from package:stats : density > image(data) [1] FALSE NULL Does this mean that the image I get is from the second file only (TAMwithamp.gpr) since that is the last one assigned to "data"? Is there any way of writing titles on the graphs / objects (with this code all that is written on the top of the image is ":image of M")? Also what does "masked from package stats" mean? Appologies for writing such a long post and asking so many questions... Looking forward to any replies and suggestions, Amy. ------------------------------------------- Amy Mikhail Research student University of Aberdeen Zoology Building Tillydrone Avenue Aberdeen AB24 2TZ Scotland Email: a.mikhail at abdn.ac.uk Phone: 00-44-1224-272880 (lab) _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
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Hi Agnes, When I carry out the list function this is what is in my environment: > ls() [1] "data" "datadir" "last.warning" [4] "lymphenoData" "mossiedata.gnames" "mossiedataTargets" [7] "mraw" "path" I tried all three of your suggestions for reading in mraw - the first two worked {> mraw <- read.GenePix(fnames="TAMwithamp.gpr") and > mraw <- read.GenePix()} but with the third option I get an error message: > mraw <- read.GenePix(fnames=c("TAMnoamp.gpr", " TAMwithamp.gpr")) Reading ... TAMnoamp.gpr Reading ... TAMwithamp.gpr Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file ' TAMwithamp.gpr' Why would there now be a problem opening "TAMwithamp.gpr" when it worked with the other two methods? Also unfortunately I still can't get maQuality plots to work. This is what happens when I try: > maQualityPlots(mraw) Error in seq.default(0, 1, length = min(17, maxcnt)) : length must be non-negative number In addition: Warning message: no finite arguments to max; returning -Inf What does this mean? Is there data missing? FYI, both of these slides are tests - self hybridisations from two colour arrays, i.e. we were hoping for lots of yellow spots if everything worked. The first one (TAMnoamp.gpr) is where the sample was prepared without a hybridisation step - actually the signal is pretty awful with the majority of spots flagged "bad", so I would not have been quite so surprised if the above error message had appeared for this file. For the second slide (TAMwithamp.gpr) the probe was prepared with an amplification step and the resulting signal is much, much better, also no spots were flagged as "bad". So what's the error message referring to? Cheers, Amy. ---------------------------------------------------------------------- ----- > Hi Amy, > > I haven't looked at the vignette you are using, so I will try to answer > your questions in a general way. > > The error message " Error in inherits(x, "factor") : Object "mraw" not > found" means that the object "mraw" does not exist in your working > environment. You can check what objects are in your environment using > the command ls(). maQualityPlots takes as argument a marrayRaw or > marrayNorm object created for example using read.GenePix. In your case, > you will need to do something like: > > mraw <- read.GenePix(fnames="TAMwithamp.gpr") > maQualityPlots(mraw) > > This command will only read the file names TAMwithamp.gpr. If you want > to read in all gpr files that are in your working directory, you can for > example either not specify any file names: > > mraw <- read.GenePix() > > or specify all files names: > > mraw <- read.GenePix(fnames=c("TAMnoamp.gpr", " TAMwithamp.gpr")) > > "masked from package stats" means that the function "density" from > package "stats" is overwriting the "density" function in package > "mclust". It shouldn't be any problem here. > > I hope this will help. If you have any other questions about > maQualityPlots, please let me know. > > Regards, > > Agnes > ---------------------------------------------------------------------- ----- > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Amy Mikhail > Sent: Monday, July 25, 2005 12:40 PM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Problems loading mraw > > Dear all, > > I am new to R and currently trying to follow some vignettes, swapping > the > example files for my own data. > > I am using R 2.1.0, Bioconductor I have downloaded from a CD provided at > the (recent) microarray analysis course in Bressanone, Italy. > > I've been trying to work through various parts of the following > vignettes: > > (a) "Quick start guide for marray" > (b) "Introduction to the Bioconductor marray package: Input component" > > So far I can import and read my files ok, but have had problems with the > the following: > >> maQualityPlots(mraw) > > I was originally getting a "colorspace not found" error message similar > to > that of Naomi's post, so I downloaded the package from the website that > was indicated in one of her replies. > > But now I'm getting a new error message: > >> maQualityPlots(mraw) > Loading required package: hexbin > Loading required package: grid > Loading required package: colorspace > > Attaching package: 'colorspace' > > > The following object(s) are masked from package:grDevices : > > hcl > > Error in inherits(x, "factor") : Object "mraw" not found > > Does this mean there is something else I should download? Would you > suggest I download all of bioconductor again, or just look for that > particular passage? > > On a separate note, I did manage to create an image of my data but am > having a bit of trouble working out which slide it is coming from; I > have > read in two .gpr files, "TAMnoamp.gpr" and "TAMwithamp.gpr": > >> library("marray") >> dir(system.file("mossiedata",package="marray")) > [1] "MMC2_grid.gal" "mossieData.txt" "TAMnoamp.gpr" "TAMwithamp.gpr" >> datadir<-system.file("mossiedata",package="marray") >> setwd(datadir) >> > mossiedataTargets<-read.marrayInfo(file.path(datadir,"mossieData.txt ")) >> data<-read.GenePix(fnames="TAMnoamp.gpr") > Reading ... TAMnoamp.gpr >> data<-read.GenePix(fnames="TAMwithamp.gpr") > Reading ... TAMwithamp.gpr >> mossiedata.gnames<-read.marrayInfo(file.path(datadir,"MMC2_grid.gal"), > + info.id=4:5,labels=5,skip=30) >> summary(mossiedata.gnames) > Object of class marrayInfo. > > maLabels Name ID > 1 Cal. 01 cYIR01 Cal. 01 > 2 Cal. 04 cYIR04 Cal. 04 > 3 Cal. 07 cYIR07 Cal. 07 > 4 Cal. 10 cYIR10 Cal. 10 > 5 Cal. 01 cYIR01 Cal. 01 > 6 Cal. 04 cYIR04 Cal. 04 > 7 Cal. 07 cYIR07 Cal. 07 > 8 Cal. 10 cYIR10 Cal. 10 > 9 Cal. 03 cYIR03 Cal. 03 > 10 Cal. 05 cYIR05 Cal. 05 > ... > > Number of labels: 13440 > Dimensions of maInfo matrix: 13440 rows by 2 columns > > Notes: > C:/PROGRA~1/R/rw2010/library/marray/mossiedata/MMC2_grid.gal >> library(arrayQuality) > Loading required package: convert > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > [1] "arrayQuality" > [1] "Checking for missing packages" > Garbage collection 135 = 74+19+42 (level 2) ... > 809344 cons cells free (67%) > 15.1 Mbytes of heap free (78%) > [1] "Loading required packages" > > Attaching package: 'mclust' > > > The following object(s) are masked from package:stats : > > density > >> image(data) > [1] FALSE > NULL > > Does this mean that the image I get is from the second file only > (TAMwithamp.gpr) since that is the last one assigned to "data"? > > Is there any way of writing titles on the graphs / objects (with this > code > all that is written on the top of the image is ":image of M")? > > Also what does "masked from package stats" mean? > > Appologies for writing such a long post and asking so many questions... > > Looking forward to any replies and suggestions, > > Amy. > > ------------------------------------------- > Amy Mikhail > Research student > University of Aberdeen > Zoology Building > Tillydrone Avenue > Aberdeen AB24 2TZ > Scotland > Email: a.mikhail at abdn.ac.uk > Phone: 00-44-1224-272880 (lab) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > >
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Sorry, there was a typo in that last explanation - TAMnoamp has no amplification step (obviously it was hybridised to the slide!) Cheers, Amy. ---------------------------------------------------------------------- ----- > Hi Agnes, > > When I carry out the list function this is what is in my environment: > >> ls() > [1] "data" "datadir" "last.warning" > [4] "lymphenoData" "mossiedata.gnames" "mossiedataTargets" > [7] "mraw" "path" > > I tried all three of your suggestions for reading in mraw - the first two > worked {> mraw <- read.GenePix(fnames="TAMwithamp.gpr") and >> mraw <- read.GenePix()} but with the third option I get an error >> message: > >> mraw <- read.GenePix(fnames=c("TAMnoamp.gpr", " TAMwithamp.gpr")) > Reading ... TAMnoamp.gpr > Reading ... TAMwithamp.gpr > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file ' TAMwithamp.gpr' > > Why would there now be a problem opening "TAMwithamp.gpr" when it worked > with the other two methods? > > Also unfortunately I still can't get maQuality plots to work. This is > what happens when I try: > >> maQualityPlots(mraw) > Error in seq.default(0, 1, length = min(17, maxcnt)) : > length must be non-negative number > In addition: Warning message: > no finite arguments to max; returning -Inf > > What does this mean? Is there data missing? > > FYI, both of these slides are tests - self hybridisations from two colour > arrays, i.e. we were hoping for lots of yellow spots if everything worked. > The first one (TAMnoamp.gpr) is where the sample was prepared without a > hybridisation step - actually the signal is pretty awful with the majority > of spots flagged "bad", so I would not have been quite so surprised if the > above error message had appeared for this file. > > For the second slide (TAMwithamp.gpr) the probe was prepared with an > amplification step and the resulting signal is much, much better, also no > spots were flagged as "bad". So what's the error message referring to? > > Cheers, > Amy. > > -------------------------------------------------------------------- ------- >> Hi Amy, >> >> I haven't looked at the vignette you are using, so I will try to answer >> your questions in a general way. >> >> The error message " Error in inherits(x, "factor") : Object "mraw" not >> found" means that the object "mraw" does not exist in your working >> environment. You can check what objects are in your environment using >> the command ls(). maQualityPlots takes as argument a marrayRaw or >> marrayNorm object created for example using read.GenePix. In your case, >> you will need to do something like: >> >> mraw <- read.GenePix(fnames="TAMwithamp.gpr") >> maQualityPlots(mraw) >> >> This command will only read the file names TAMwithamp.gpr. If you want >> to read in all gpr files that are in your working directory, you can for >> example either not specify any file names: >> >> mraw <- read.GenePix() >> >> or specify all files names: >> >> mraw <- read.GenePix(fnames=c("TAMnoamp.gpr", " TAMwithamp.gpr")) >> >> "masked from package stats" means that the function "density" from >> package "stats" is overwriting the "density" function in package >> "mclust". It shouldn't be any problem here. >> >> I hope this will help. If you have any other questions about >> maQualityPlots, please let me know. >> >> Regards, >> >> Agnes >> > -------------------------------------------------------------------- ------- >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch >> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Amy Mikhail >> Sent: Monday, July 25, 2005 12:40 PM >> To: bioconductor at stat.math.ethz.ch >> Subject: [BioC] Problems loading mraw >> >> Dear all, >> >> I am new to R and currently trying to follow some vignettes, swapping >> the >> example files for my own data. >> >> I am using R 2.1.0, Bioconductor I have downloaded from a CD provided at >> the (recent) microarray analysis course in Bressanone, Italy. >> >> I've been trying to work through various parts of the following >> vignettes: >> >> (a) "Quick start guide for marray" >> (b) "Introduction to the Bioconductor marray package: Input component" >> >> So far I can import and read my files ok, but have had problems with the >> the following: >> >>> maQualityPlots(mraw) >> >> I was originally getting a "colorspace not found" error message similar >> to >> that of Naomi's post, so I downloaded the package from the website that >> was indicated in one of her replies. >> >> But now I'm getting a new error message: >> >>> maQualityPlots(mraw) >> Loading required package: hexbin >> Loading required package: grid >> Loading required package: colorspace >> >> Attaching package: 'colorspace' >> >> >> The following object(s) are masked from package:grDevices : >> >> hcl >> >> Error in inherits(x, "factor") : Object "mraw" not found >> >> Does this mean there is something else I should download? Would you >> suggest I download all of bioconductor again, or just look for that >> particular passage? >> >> On a separate note, I did manage to create an image of my data but am >> having a bit of trouble working out which slide it is coming from; I >> have >> read in two .gpr files, "TAMnoamp.gpr" and "TAMwithamp.gpr": >> >>> library("marray") >>> dir(system.file("mossiedata",package="marray")) >> [1] "MMC2_grid.gal" "mossieData.txt" "TAMnoamp.gpr" "TAMwithamp.gpr" >>> datadir<-system.file("mossiedata",package="marray") >>> setwd(datadir) >>> >> mossiedataTargets<-read.marrayInfo(file.path(datadir,"mossieData.tx t")) >>> data<-read.GenePix(fnames="TAMnoamp.gpr") >> Reading ... TAMnoamp.gpr >>> data<-read.GenePix(fnames="TAMwithamp.gpr") >> Reading ... TAMwithamp.gpr >>> mossiedata.gnames<-read.marrayInfo(file.path(datadir,"MMC2_grid.gal"), >> + info.id=4:5,labels=5,skip=30) >>> summary(mossiedata.gnames) >> Object of class marrayInfo. >> >> maLabels Name ID >> 1 Cal. 01 cYIR01 Cal. 01 >> 2 Cal. 04 cYIR04 Cal. 04 >> 3 Cal. 07 cYIR07 Cal. 07 >> 4 Cal. 10 cYIR10 Cal. 10 >> 5 Cal. 01 cYIR01 Cal. 01 >> 6 Cal. 04 cYIR04 Cal. 04 >> 7 Cal. 07 cYIR07 Cal. 07 >> 8 Cal. 10 cYIR10 Cal. 10 >> 9 Cal. 03 cYIR03 Cal. 03 >> 10 Cal. 05 cYIR05 Cal. 05 >> ... >> >> Number of labels: 13440 >> Dimensions of maInfo matrix: 13440 rows by 2 columns >> >> Notes: >> C:/PROGRA~1/R/rw2010/library/marray/mossiedata/MMC2_grid.gal >>> library(arrayQuality) >> Loading required package: convert >> Loading required package: Biobase >> Loading required package: tools >> Welcome to Bioconductor >> Vignettes contain introductory material. To view, >> simply type: openVignette() >> For details on reading vignettes, see >> the openVignette help page. >> [1] "arrayQuality" >> [1] "Checking for missing packages" >> Garbage collection 135 = 74+19+42 (level 2) ... >> 809344 cons cells free (67%) >> 15.1 Mbytes of heap free (78%) >> [1] "Loading required packages" >> >> Attaching package: 'mclust' >> >> >> The following object(s) are masked from package:stats : >> >> density >> >>> image(data) >> [1] FALSE >> NULL >> >> Does this mean that the image I get is from the second file only >> (TAMwithamp.gpr) since that is the last one assigned to "data"? >> >> Is there any way of writing titles on the graphs / objects (with this >> code >> all that is written on the top of the image is ":image of M")? >> >> Also what does "masked from package stats" mean? >> >> Appologies for writing such a long post and asking so many questions... >> >> Looking forward to any replies and suggestions, >> >> Amy. >> >> ------------------------------------------- >> Amy Mikhail >> Research student >> University of Aberdeen >> Zoology Building >> Tillydrone Avenue >> Aberdeen AB24 2TZ >> Scotland >> Email: a.mikhail at abdn.ac.uk >> Phone: 00-44-1224-272880 (lab) >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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Paquet, Agnes ▴ 500
@paquet-agnes-807
Last seen 9.6 years ago
Hi Amy, There is an extra space in the 2nd file name, that's why it's not found. You should use something like" mraw <- read.GenePix(fnames=c("TAMnoamp.gpr", "TAMwithamp.gpr")) The error you are getting in maQualityPlots happens sometimes when control spots are not defined properly. By default, they are set to the control spots we use in my lab. You can check arrayQuality user guide for instructions about how to set up your own controls. You can also refer to help files for maControls and maGenControls in the marray package. There are several ways to set up your controls. The easiest way is to set the R object controlCode to your own controls using readcontrolCode(), and then read in your files and generate the quality plots. If this doesn't work, could you please send me one of your gpr files and a spot type file (a tab-delimited text file containing your controls types) so that I can fix the error? Cheers, Agnes -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Amy Mikhail Sent: Tuesday, July 26, 2005 10:50 AM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Problems loading mraw Hi Agnes, When I carry out the list function this is what is in my environment: > ls() [1] "data" "datadir" "last.warning" [4] "lymphenoData" "mossiedata.gnames" "mossiedataTargets" [7] "mraw" "path" I tried all three of your suggestions for reading in mraw - the first two worked {> mraw <- read.GenePix(fnames="TAMwithamp.gpr") and > mraw <- read.GenePix()} but with the third option I get an error message: > mraw <- read.GenePix(fnames=c("TAMnoamp.gpr", " TAMwithamp.gpr")) Reading ... TAMnoamp.gpr Reading ... TAMwithamp.gpr Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file ' TAMwithamp.gpr' Why would there now be a problem opening "TAMwithamp.gpr" when it worked with the other two methods? Also unfortunately I still can't get maQuality plots to work. This is what happens when I try: > maQualityPlots(mraw) Error in seq.default(0, 1, length = min(17, maxcnt)) : length must be non-negative number In addition: Warning message: no finite arguments to max; returning -Inf What does this mean? Is there data missing? FYI, both of these slides are tests - self hybridisations from two colour arrays, i.e. we were hoping for lots of yellow spots if everything worked. The first one (TAMnoamp.gpr) is where the sample was prepared without a hybridisation step - actually the signal is pretty awful with the majority of spots flagged "bad", so I would not have been quite so surprised if the above error message had appeared for this file. For the second slide (TAMwithamp.gpr) the probe was prepared with an amplification step and the resulting signal is much, much better, also no spots were flagged as "bad". So what's the error message referring to? Cheers, Amy. ---------------------------------------------------------------------- -- --- > Hi Amy, > > I haven't looked at the vignette you are using, so I will try to answer > your questions in a general way. > > The error message " Error in inherits(x, "factor") : Object "mraw" not > found" means that the object "mraw" does not exist in your working > environment. You can check what objects are in your environment using > the command ls(). maQualityPlots takes as argument a marrayRaw or > marrayNorm object created for example using read.GenePix. In your case, > you will need to do something like: > > mraw <- read.GenePix(fnames="TAMwithamp.gpr") > maQualityPlots(mraw) > > This command will only read the file names TAMwithamp.gpr. If you want > to read in all gpr files that are in your working directory, you can for > example either not specify any file names: > > mraw <- read.GenePix() > > or specify all files names: > > mraw <- read.GenePix(fnames=c("TAMnoamp.gpr", " TAMwithamp.gpr")) > > "masked from package stats" means that the function "density" from > package "stats" is overwriting the "density" function in package > "mclust". It shouldn't be any problem here. > > I hope this will help. If you have any other questions about > maQualityPlots, please let me know. > > Regards, > > Agnes > ---------------------------------------------------------------------- -- --- > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Amy Mikhail > Sent: Monday, July 25, 2005 12:40 PM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Problems loading mraw > > Dear all, > > I am new to R and currently trying to follow some vignettes, swapping > the > example files for my own data. > > I am using R 2.1.0, Bioconductor I have downloaded from a CD provided at > the (recent) microarray analysis course in Bressanone, Italy. > > I've been trying to work through various parts of the following > vignettes: > > (a) "Quick start guide for marray" > (b) "Introduction to the Bioconductor marray package: Input component" > > So far I can import and read my files ok, but have had problems with the > the following: > >> maQualityPlots(mraw) > > I was originally getting a "colorspace not found" error message similar > to > that of Naomi's post, so I downloaded the package from the website that > was indicated in one of her replies. > > But now I'm getting a new error message: > >> maQualityPlots(mraw) > Loading required package: hexbin > Loading required package: grid > Loading required package: colorspace > > Attaching package: 'colorspace' > > > The following object(s) are masked from package:grDevices : > > hcl > > Error in inherits(x, "factor") : Object "mraw" not found > > Does this mean there is something else I should download? Would you > suggest I download all of bioconductor again, or just look for that > particular passage? > > On a separate note, I did manage to create an image of my data but am > having a bit of trouble working out which slide it is coming from; I > have > read in two .gpr files, "TAMnoamp.gpr" and "TAMwithamp.gpr": > >> library("marray") >> dir(system.file("mossiedata",package="marray")) > [1] "MMC2_grid.gal" "mossieData.txt" "TAMnoamp.gpr" "TAMwithamp.gpr" >> datadir<-system.file("mossiedata",package="marray") >> setwd(datadir) >> > mossiedataTargets<-read.marrayInfo(file.path(datadir,"mossieData.txt") ) >> data<-read.GenePix(fnames="TAMnoamp.gpr") > Reading ... TAMnoamp.gpr >> data<-read.GenePix(fnames="TAMwithamp.gpr") > Reading ... TAMwithamp.gpr >> mossiedata.gnames<-read.marrayInfo(file.path(datadir,"MMC2_grid.gal"), > + info.id=4:5,labels=5,skip=30) >> summary(mossiedata.gnames) > Object of class marrayInfo. > > maLabels Name ID > 1 Cal. 01 cYIR01 Cal. 01 > 2 Cal. 04 cYIR04 Cal. 04 > 3 Cal. 07 cYIR07 Cal. 07 > 4 Cal. 10 cYIR10 Cal. 10 > 5 Cal. 01 cYIR01 Cal. 01 > 6 Cal. 04 cYIR04 Cal. 04 > 7 Cal. 07 cYIR07 Cal. 07 > 8 Cal. 10 cYIR10 Cal. 10 > 9 Cal. 03 cYIR03 Cal. 03 > 10 Cal. 05 cYIR05 Cal. 05 > ... > > Number of labels: 13440 > Dimensions of maInfo matrix: 13440 rows by 2 columns > > Notes: > C:/PROGRA~1/R/rw2010/library/marray/mossiedata/MMC2_grid.gal >> library(arrayQuality) > Loading required package: convert > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > [1] "arrayQuality" > [1] "Checking for missing packages" > Garbage collection 135 = 74+19+42 (level 2) ... > 809344 cons cells free (67%) > 15.1 Mbytes of heap free (78%) > [1] "Loading required packages" > > Attaching package: 'mclust' > > > The following object(s) are masked from package:stats : > > density > >> image(data) > [1] FALSE > NULL > > Does this mean that the image I get is from the second file only > (TAMwithamp.gpr) since that is the last one assigned to "data"? > > Is there any way of writing titles on the graphs / objects (with this > code > all that is written on the top of the image is ":image of M")? > > Also what does "masked from package stats" mean? > > Appologies for writing such a long post and asking so many questions... > > Looking forward to any replies and suggestions, > > Amy. > > ------------------------------------------- > Amy Mikhail > Research student > University of Aberdeen > Zoology Building > Tillydrone Avenue > Aberdeen AB24 2TZ > Scotland > Email: a.mikhail at abdn.ac.uk > Phone: 00-44-1224-272880 (lab) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
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