Question: FW: makecdfenv()
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gravatar for Lana Schaffer
14.7 years ago by
Lana Schaffer80 wrote:
Greetings, Can someone tell me how to use 'pipes' from R to send the output of my process to a file? ie. make.cdf.package(.....) | ?? Lana -----Original Message----- From: Laurent Gautier [mailto:lgautier@altern.org] Sent: Wednesday, July 14, 2004 7:25 PM To: Lana Schaffer Subject: Re: [BioC] makecdfenv() >>Now I can add: >>- go to the C source of the parser, turn the debug/verbose switch on and >>recompile/install the pack (then the parser will be _very_ verbose). > > > I turned on _very_verbose in the C code and did the recompile/install. Now > the output goes to the screen, but how to put the "very verbose" output to > a file?? what about using 'pipes' to send the output of your process to a file ? > Lana > > > > > -----Original Message----- > From: Laurent Gautier [mailto:lgautier@altern.org] > Sent: Tuesday, July 13, 2004 6:30 AM > To: Robert Gentleman > Cc: Lana Schaffer > Subject: Re: [BioC] makecdfenv() > > > Robert Gentleman wrote: > >>I think you need to provide a little more detail than that. >> >>Which gene is skipped? >> >>It could have something to do with the reading of lines with comment >>characters in them (especially if there is only one gene skipped). >>Or it could have to do with there being ' (single quotes) in the gene >>names. >> >>scan, read.table etc all have notions of comment.char and of what >>quotes are (and how to interpret them), > > > > Robert, > > > I believe that Lana refers to the function read.cdffile. That function > calls C level parsers written to parse Affymetrix genuine CDF files. > Writting a R level level function, using itself R functions such as > 'scan' would have been possible (and actually was tried when I first > wrote the parsers, now 3 years ago). I quickly (i.e., before it left my > hd) moved the code to C to improve speed (CDF file can be quite large). > > What Lana does not specify in her mail is that she uses a 'home- made' > CDF file. She already had trouble with her CDF, but apparently managed > to overcome this. I included few consistency checks in the parser but > not enough to detect everything. Lana did not tell us _how_ she built > her custom CDF, which limits the amount of help I can provide. > > As before, I would recommend her to: > - explain what she want to achieve with a custom CDF > - have a look at the pack makecdfenvs (note that the devel version of > altcdfenvs has a vignette with the Affymetrix malaria/anopheles chip, > and we have a documentation in a non-vignette form (submitted paper)). > Now I can add: > - go to the C source of the parser, turn the debug/verbose switch on and > recompile/install the pack (then the parser will be _very_ verbose). > > > Hopin' it helps, > > > > L. > > > > > > >> Robert >> >> >> >>On Mon, Jul 12, 2004 at 04:40:06PM -0700, Lana Schaffer wrote: >> >> >>>Hi, >>>I am using R-1.9.1 and makecdfenv-1.4.7 and 1.4.1, but found that in reading >>>my CDF file a gene gets skipped. Does anyone know why this could happen? >>>Lana >>> >>>_______________________________________________ >>>Bioconductor mailing list >>>Bioconductor@stat.math.ethz.ch >>>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >> >> > >
go cdf process altcdfenvs • 413 views
ADD COMMENTlink written 14.7 years ago by Lana Schaffer80
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