[prev in list] [next in list] [prev in thread] [next in thread]
List: bioconductor
Subject: Re: [BioC] package charm, creating .xys files
From: "Li,Johnny Qinghong,ST. LOUIS,NRC St. Louis Petcare" <Qinghong.Li () rd ! nestle ! com>
Date: 2012-01-31 16:27:02
Message-ID: 5F9829AB5D913F41BCD6044FBF5F674901ADEAEC () USPHXE0016 ! nestle ! com
[Download RAW message or body]
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]]
_______________________________________________
Bioconductor mailing list
Bioconductor@r-project.org
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
[prev in list] [next in list] [prev in thread] [next in thread]
Configure |
About |
News |
Add a list |
Sponsored by KoreLogic