Question: oligo and pdInfoBuilder
0
gravatar for Simon Melov
7.4 years ago by
Simon Melov340
Simon Melov340 wrote:
I've been beating my head against the wall for several hours trying to see why I cant build a library for a nimblegen expression array, using the oligo and pdInfoBuilder packages. I dont see any errors when building the library for a 12plex yeast genome expression array.... makePdInfoPackage(seed, destDir = "/Library/Frameworks/R.framework/Versions/2.15/Resources/library/") ====================================================================== ========== Building annotation package for Nimblegen Expression Array NDF: 100718_Scer_EXP.ndf XYS: 532785A01_Chip6.330.2012.5.8_532.xys ====================================================================== ========== Parsing file: 100718_Scer_EXP.ndf... OK Parsing file: 532785A01_Chip6.330.2012.5.8_532.xys... OK Merging NDF and XYS files... OK Preparing contents for featureSet table... OK Preparing contents for bgfeature table... OK Preparing contents for pmfeature table... OK Creating package in /Library/Frameworks/R.framework/Versions/2.15/Reso urces/library//pd.100718.scer.exp Inserting 5777 rows into table featureSet... OK Inserting 137040 rows into table pmfeature... OK Counting rows in featureSet Counting rows in pmfeature Creating index idx_pmfsetid on pmfeature... OK Creating index idx_pmfid on pmfeature... OK Creating index idx_fsfsetid on featureSet... OK Saving DataFrame object for PM. Done. > but when I try to use the library in oligo, it fails for some reason library(pd.100718.scer.exp) Error in library(pd.100718.scer.exp) : 'pd.100718.scer.exp' is not a valid installed package > Can anyone help? I'm at my wits end...
ADD COMMENTlink modified 7.4 years ago by Vincent J. Carey, Jr.6.3k • written 7.4 years ago by Simon Melov340
Answer: oligo and pdInfoBuilder
0
gravatar for Vincent J. Carey, Jr.
7.4 years ago by
United States
Vincent J. Carey, Jr.6.3k wrote:
On Sun, Jun 3, 2012 at 11:08 PM, Simon Melov <smelov@buckinstitute.org>wrote: > I've been beating my head against the wall for several hours trying to see > why I cant build a library for a nimblegen expression array, using the > oligo and pdInfoBuilder packages. I dont see any errors when building the > library for a 12plex yeast genome expression array.... > > makePdInfoPackage(seed, destDir = > "/Library/Frameworks/R.framework/Versions/2.15/Resources/library/") > > ==================================================================== ============ > Building annotation package for Nimblegen Expression Array > NDF: 100718_Scer_EXP.ndf > XYS: 532785A01_Chip6.330.2012.5.8_532.xys > > ==================================================================== ============ > Parsing file: 100718_Scer_EXP.ndf... OK > Parsing file: 532785A01_Chip6.330.2012.5.8_532.xys... OK > Merging NDF and XYS files... OK > Preparing contents for featureSet table... OK > Preparing contents for bgfeature table... OK > Preparing contents for pmfeature table... OK > Creating package in > /Library/Frameworks/R.framework/Versions/2.15/Resources/library//pd. 100718.scer.exp > Inserting 5777 rows into table featureSet... OK > Inserting 137040 rows into table pmfeature... OK > Counting rows in featureSet > Counting rows in pmfeature > Creating index idx_pmfsetid on pmfeature... OK > Creating index idx_pmfid on pmfeature... OK > Creating index idx_fsfsetid on featureSet... OK > Saving DataFrame object for PM. > Done. > > > > but when I try to use the library in oligo, it fails for some reason > > library(pd.100718.scer.exp) > Error in library(pd.100718.scer.exp) : > 'pd.100718.scer.exp' is not a valid installed package > What happened when you ran R CMD INSTALL (or install.packages?) sessionInfo()? > > > > Can anyone help? I'm at my wits end... > _______________________________________________ > 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 > [[alternative HTML version deleted]]
ADD COMMENTlink written 7.4 years ago by Vincent J. Carey, Jr.6.3k
That was it, Ben set me straight, sorry for the time waster! On Jun 3, 2012, at 8:33 PM, Vincent Carey wrote: On Sun, Jun 3, 2012 at 11:08 PM, Simon Melov <smelov at="" buckinstitute.org<mailto:smelov="" at="" buckinstitute.org="">> wrote: I've been beating my head against the wall for several hours trying to see why I cant build a library for a nimblegen expression array, using the oligo and pdInfoBuilder packages. I dont see any errors when building the library for a 12plex yeast genome expression array.... makePdInfoPackage(seed, destDir = "/Library/Frameworks/R.framework/Versions/2.15/Resources/library/") ====================================================================== ========== Building annotation package for Nimblegen Expression Array NDF: 100718_Scer_EXP.ndf XYS: 532785A01_Chip6.330.2012.5.8_532.xys ====================================================================== ========== Parsing file: 100718_Scer_EXP.ndf... OK Parsing file: 532785A01_Chip6.330.2012.5.8_532.xys... OK Merging NDF and XYS files... OK Preparing contents for featureSet table... OK Preparing contents for bgfeature table... OK Preparing contents for pmfeature table... OK Creating package in /Library/Frameworks/R.framework/Versions/2.15/Reso urces/library//pd.100718.scer.exp Inserting 5777 rows into table featureSet... OK Inserting 137040 rows into table pmfeature... OK Counting rows in featureSet Counting rows in pmfeature Creating index idx_pmfsetid on pmfeature... OK Creating index idx_pmfid on pmfeature... OK Creating index idx_fsfsetid on featureSet... OK Saving DataFrame object for PM. Done. > but when I try to use the library in oligo, it fails for some reason library(pd.100718.scer.exp) Error in library(pd.100718.scer.exp) : 'pd.100718.scer.exp' is not a valid installed package What happened when you ran R CMD INSTALL (or install.packages?) sessionInfo()? > Can anyone help? I'm at my wits end... _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 7.4 years ago by Simon Melov340
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 222 users visited in the last hour