Question: readGenericHeader problem in limma 2.7.8?
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gravatar for Bobby Prill
13.3 years ago by
Bobby Prill60
Bobby Prill60 wrote:
There seems to be a problem with read.maimages() in the current release version of bioconductor (1.8). I need load a "generic" gpr- like file using the column headers. The following code used to work, but now is broken: library(limma) cols = list(Rf="F635 Median",Gf="F532 Median",Rb="B635 Median",Gb="B532 Median") RG = read.maimages("mydata.gpr", columns=cols) Is this a bug? How can I get around this problem? I have tried limma version 2.7.8 and 2.7.9 I'm on a Mac OSX 10.4.7 Running R.app 1.16 The error message is: Error in readGenericHeader(fullname, columns = columns, sep = sep) : Specified column headings not found in file In addition: Warning message: input string 1 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) Even though it says it can't find the headers, I know they are there. This error started to occur when I installed a fresh copy of Bioconductor 1.8 after my disk crashed. I was probably running 1.7 before that. I don't know how to attempt an install of 1.7 to see if that affects anything. Thanks for the help.
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ADD COMMENTlink modified 13.3 years ago by Marcus Davy680 • written 13.3 years ago by Bobby Prill60
Answer: readGenericHeader problem in limma 2.7.8?
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gravatar for Marcus Davy
13.3 years ago by
Marcus Davy680
Marcus Davy680 wrote:
Relating to your question, > I don't know how to attempt an install of 1.7 to see if that affects > anything. You want to use limma which does not have any critical package dependencies so you don't need BioC 1.7 unless you want to use other classes and methods than that provided in limma. Using OS X, to examine different versions of limma quickly, one option is to reinstall a recent previous R.app dmg package major release of R (e.g. Compare limma between R-2.2.1, and R-2.3.1) at the system level and install a previous version of limma that you think works to test if it is a limma version problem. Then you can just quickly change R versions to examine different limma versions on a test script. Reinstallation does not effect any contributed packages you have previously installed for a particular version of R which are located in; /Library/Frameworks/R.framework/Versions/Current/Resources/library (Current directory is a symbolic pointer) You just need to make sure that the contributed package your are installing (limma version) is compatible across the recent major versions of R you want to test with. If you were installing lots of packages this would not be recommended, but since it is only one which has no critical dependencies you should be ok. The releases of R will go into; ls -la /Library/Frameworks/R.framework/Versions/ drwxrwxr-x 9 root admin 306 Jul 27 16:44 . drwxrwxr-x 8 root admin 272 Jul 27 16:44 .. -rw-rw-r-- 1 root admin 6148 Oct 17 2005 .DS_Store lrwxr-xr-x 1 root admin 5 Aug 16 2005 2.1 -> 2.1.1 lrwxr-xr-x 1 root admin 5 Aug 16 2005 2.1.0 -> 2.1.1 drwxrwxr-x 4 root admin 136 Dec 14 2005 2.1.1 drwxrwxr-x 4 root admin 136 Jul 27 16:44 2.2 drwxrwxr-x 6 root admin 204 Jul 27 16:44 2.3 lrwxr-xr-x 1 root admin 3 Jul 27 16:44 Current -> 2.3 The 'Current' symbolic pointer tells you which version is currently working. So if you have a previous installation working (where 'Current' points to say version 2.2) and the latest version of R is installed but not pointed to, then it *should* just be a case of changing the symbolic link of 'Current' back to 2.3 again, e.g. sudo -s #[PASSWORD] rm /Library/Frameworks/R.framework/Versions/Current ln -s 2.3 Current but I have found that reinstallation of that particular R.app dma version is required sometimes (when the executable is not found, problem with some DMG installations perhaps?). Once again this does not effect any previously contributed package libraries you have installed for that R version, as long as you haven't specifically deleted them. In R use 'version', and 'sessionInfo()'to gather information about the current R session if errors still occur. Marcus On 8/22/06 7:12 AM, "Bobby Prill" <rprill at="" jhu.edu=""> wrote: > There seems to be a problem with read.maimages() in the current > release version of bioconductor (1.8). I need load a "generic" gpr- > like file using the column headers. > > The following code used to work, but now is broken: > > library(limma) > cols = list(Rf="F635 Median",Gf="F532 Median",Rb="B635 > Median",Gb="B532 Median") > RG = read.maimages("mydata.gpr", columns=cols) > > Is this a bug? How can I get around this problem? > > I have tried > limma version 2.7.8 and 2.7.9 > > I'm on a Mac OSX 10.4.7 > Running R.app 1.16 > > The error message is: > Error in readGenericHeader(fullname, columns = columns, sep = sep) : > Specified column headings not found in file > In addition: Warning message: > input string 1 is invalid in this locale in: grep(pattern, x, > ignore.case, extended, value, fixed, useBytes) > > Even though it says it can't find the headers, I know they are > there. This error started to occur when I installed a fresh copy of > Bioconductor 1.8 after my disk crashed. I was probably running 1.7 > before that. > > I don't know how to attempt an install of 1.7 to see if that affects > anything. > > Thanks for the help. > > _______________________________________________ > 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 ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}
ADD COMMENTlink written 13.3 years ago by Marcus Davy680
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