Hi Benilton, Thanks for trouble shooting. I played a little bit with the script. I first tried to make sure I do have permission to write (see below). Then I ran the script as directed, got the error message (1) as shown earlier. I ran a second time, I got error message (2, in red). So add unlink=TRUE, re-ran it, still got error (2). Then I manually deleted the folder "pd.090806.rn34.deluxe.promoter.hx1" under C:/, re-ran it, it went back to error message (1). I also tried to make sure I can write to folder "pd.090806.rn34.deluxe.promoter.hx1" by writing matrix a to it. It is writable. I am not sure if this is specific to window version of R? Based on your experience, if everytihig is OK'ed all the way to parsing xys file, and the script is trying to create package, it should went well? As a matter of fact, a fold named "pd.090806.rn34.deluxe.promoter.hx1 " was created with some sub folders inside. Best Regards, Johnny > setwd("C:/") > getwd() [1] "C:/" > a<-matrix(1:20, nrow=4) > write.csv(x=a, file="a.csv") > getwd() [1] "C:/" > makePdInfoPackage(seed, destDir=".") ====================================================================== == ======== Building annotation package for Nimblegen Tiling Array NDF: 090806_RN34_Deluxe_Promoter_HX1.ndf POS: 090806_RN34_Deluxe_Promoter_HX1.pos XYS: 65502805_532.xys ====================================================================== == ======== Parsing file: 090806_RN34_Deluxe_Promoter_HX1.ndf... OK Parsing file: 090806_RN34_Deluxe_Promoter_HX1.pos... OK Merging NDF and POS files... OK Parsing file: 65502805_532.xys... OK Creating package in ./pd.090806.rn34.deluxe.promoter.hx1 Error in sqliteNewConnection(drv, ...) : ------------------error message (1) RS-DBI driver: (could not connect to dbname: unable to open database file ) In addition: Warning message: In dir.create(extdataDir, recursive = TRUE) : cannot create dir '.', reason 'Permission denied' > makePdInfoPackage(seed, destDir=".", unlink=T) ====================================================================== == ======== Building annotation package for Nimblegen Tiling Array NDF: 090806_RN34_Deluxe_Promoter_HX1.ndf POS: 090806_RN34_Deluxe_Promoter_HX1.pos XYS: 65502805_532.xys ====================================================================== == ======== Parsing file: 090806_RN34_Deluxe_Promoter_HX1.ndf... OK Parsing file: 090806_RN34_Deluxe_Promoter_HX1.pos... OK Merging NDF and POS files... OK Parsing file: 65502805_532.xys... OK Creating package in ./pd.090806.rn34.deluxe.promoter.hx1 ----------------error message (2) Error in createPackage(pkgname = pkgName, destinationDir = destDir, originDir = templateDir, : Directory ./pd.090806.rn34.deluxe.promoter.hx1 exists. Please use unlink=TRUE to remove it or choose another destination directory. > write.csv(x=a, file="C:/a.csv") > write.csv(x=a, file="C:/pd.090806.rn34.deluxe.promoter.hx1/a.csv") > getwd() [1] "C:/" From: Benilton Carvalho [mailto:beniltoncarvalho@gmail.com] Sent: Tuesday, January 31, 2012 2:01 AM To: Li,Johnny Qinghong,ST. LOUIS,NRC St. Louis Petcare Cc: bioconductor@r-project.org Subject: Re: [BioC] package charm, creating .xys files Hi Johnny, The initial error suggests you didn't have permission to write to the current directory (whatever it was, you could have obtained that through getwd() ). The second error is slightly harder for me to understand, mostly because I don't have a windows machine.... Assuming you do have permission to write to c:\ , could you please try using destDir="c:/" An alternative is using setwd() before everything to change the current directory to somewhere you're 100% sure you can write. Then, run getwd() to ensure you're really in that directory. And, finally, run the script as you ran in the first time (ie, without modifying the destination directory). Please let me know how it goes, b On Tuesday, 31 January 2012, Li,Johnny Qinghong,ST. LOUIS,NRC St. Louis Petcare <qinghong.li@rd.nestle.com> wrote: > Hi again, > > I changed destDir="C:\" since it mentioned permission denied to dir ".", and re-ran the same script, the error message changed. > > Regards, > Johnny > >> makePdInfoPackage(seed, destDir="C:\") > ====================================================================== == ======== > Building annotation package for Nimblegen Tiling Array > NDF: 090806_RN34_Deluxe_Promoter_HX1.ndf > POS: 090806_RN34_Deluxe_Promoter_HX1.pos > XYS: 65502805_532.xys > ====================================================================== == ======== > Parsing file: 090806_RN34_Deluxe_Promoter_HX1.ndf... OK > Parsing file: 090806_RN34_Deluxe_Promoter_HX1.pos... OK > Merging NDF and POS files... OK > Parsing file: 65502805_532.xys... OK > Error in if (!file.exists(get(a)) || !file.info(get(a))$isdir) stop(paste("'", : > missing value where TRUE/FALSE needed > >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: x86_64-pc-mingw32/x64 (64-bit) > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] pdInfoBuilder_1.18.0 oligo_1.18.1 oligoClasses_1.16.0 > [4] affxparser_1.26.2 RSQLite_0.11.1 DBI_0.2-5 > [7] Biobase_2.14.0 BiocInstaller_1.2.1 > loaded via a namespace (and not attached): > [1] affyio_1.22.0 Biostrings_2.22.0 bit_1.1-8 > [4] ff_2.2-5 IRanges_1.12.5 preprocessCore_1.16.0 > [7] splines_2.14.1 tools_2.14.1 zlibbioc_1.0.0 > ________________________________ > From: bioconductor-bounces@r-project.org on behalf of Li,Johnny Qinghong,ST. LOUIS,NRC St. Louis Petcare > Sent: Tue 1/31/2012 2:36 AM > To: Benilton Carvalho > Cc: bioconductor@r-project.org > Subject: Re: [BioC] package charm, creating .xys files > > Hi Benilton, > > Thank you very much for the pointers. It is very helpful. > > I think I created the .xys file successfully. I used pdInfoBuilder to build the package, but ran into some unexpected errors. It said unable to connect to db. Do you have any idea what that means? > > Regards, > Johnny > > > >> makePdInfoPackage(seed, destDir=".") > ====================================================================== == ======== > Building annotation package for Nimblegen Tiling Array > NDF: 090806_RN34_Deluxe_Promoter_HX1.ndf > POS: 090806_RN34_Deluxe_Promoter_HX1.pos > XYS: 65502805_532.xys > ====================================================================== == ======== > Parsing file: 090806_RN34_Deluxe_Promoter_HX1.ndf... OK > Parsing file: 090806_RN34_Deluxe_Promoter_HX1.pos... OK > Merging NDF and POS files... OK > Parsing file: 65502805_532.xys... OK > Creating package in ./pd.090806.rn34.deluxe.promoter.hx1 > Error in sqliteNewConnection(drv, ...) : > RS-DBI driver: (could not connect to dbname: > unable to open database file > ) > In addition: Warning message: > In dir.create(extdataDir, recursive = TRUE) : > cannot create dir '.', reason 'Permission denied' > > > ________________________________ > > From: Benilton Carvalho [mailto:beniltoncarvalho@gmail.com] > Sent: Fri 1/27/2012 11:41 PM > To: Li,Johnny Qinghong,ST. LOUIS,NRC St. Louis Petcare > Cc: bioconductor@r-project.org > Subject: Re: [BioC] package charm, creating .xys files > > > > Hi Johnny, > > 1) The SIGNAL is the PM column; > > 2) About the controls... Look at the NDF file... All the PMs are > *expected* to have PROBE_CLASS == 'experimental' and MISMATCH == 0 > (you can double check this[*])... then, everything else is > 'control'... A shortcut that might work (never tried) is get get all > the X/Y coordinates for which you don't have readings on the PM column > of your .pair file. > > 3) Yes. > > 4) After having the 3 required columns for the XYS, remember to sort > the rows so you have something like: > > X Y SIGNAL COUNT > 1 1 <value_or_na> <value_or_na> > 1 2 <value_or_na> <value_or_na> > 1 3 <value_or_na> <value_or_na> > ...... > 2 1 <value_or_na> <value_or_na> > 2 2 <value_or_na> <value_or_na> > etc > > (download the maqcExpression4plex package and check the XYS files in > its 'extdata' directory for reference) > > HTH, > > b > > On 27 January 2012 20:46, Li,Johnny Qinghong,ST. LOUIS,NRC St. Louis > Petcare <qinghong.li@rd.nestle.com> wrote: >> Hi, >> >> >> >> I am trying to create an annotation package so I can use "charm" to >> analyze nimblegen rat data. We have only .pair files but the .tiff >> files. So won't be able to generate the .xys files using NimbleScan. >> >> >> >> I have a few questions: >> >> 1. what does the SIGNAL column in .xys file come from? Is it the >> PM column in the .pair file? >> >> 2. I was told all control probes have NAs in both SIGNAL and >> COUNT, how do I know which ones are control? >> >> 3. I assume X Y columns are the same in both pair and xys files? >> >> >> >> Here is the old threat on similar topic: >> http://answerpot.com/showthread.php?662032-XYS+from+nimblegen >> >> >> >> Thanks, >> >> Johnny >> >> >> >> >> >> >> >> >> >> >> >> >> >> ****** >> >> Johnny Li, Ph.D. >> >> Nestle Purina PetCare Company >> >> Saint Louis, MO 63164 >> >> >> >> Tel: (314) 982-2295 >> >> Fax: (314) 982-5857 >> >> Email: qinghong.li@rd.nestle.com >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> [[alternative HTML version deleted]]