How to get the relative path with list.celfiles() from the oligo package?
2
0
Entering edit mode
Peng Yu ▴ 940
@peng-yu-3586
Last seen 10.3 years ago
Hi, I run the following command. But it only gives the file names. I am wondering if there is a way to get the filename along with the directory name, i.e., 'data/ki10923.CEL', etc. Regards, Peng > list.celfiles('data/') [1] "ki10923.CEL" "ki10924.CEL" "ki10925.CEL" "ki10926.CEL" "ki10928.CEL" [6] "wt10921.CEL" "wt10922.CEL" "wt10927.CEL" "wt10930.CEL" "wt10980.CEL"
• 2.4k views
ADD COMMENT •
0
Entering edit mode
@sean-davis-490
Last seen 4 months ago
United States
On Thu, Aug 20, 2009 at 4:24 PM, Peng Yu <pengyu.ut@gmail.com> wrote: > Hi, > > I run the following command. But it only gives the file names. I am > wondering if there is a way to get the filename along with the > directory name, i.e., 'data/ki10923.CEL', etc. > > Regards, > Peng > > > list.celfiles('data/') > [1] "ki10923.CEL" "ki10924.CEL" "ki10925.CEL" "ki10926.CEL" "ki10928.CEL" > [6] "wt10921.CEL" "wt10922.CEL" "wt10927.CEL" "wt10930.CEL" "wt10980.CEL" > Hi, Peng. Reading the help for list.celfiles(), it suggests that all arguments are passed along to the list.files(). Reading the help for list.files() suggests that including full.names=TRUE will return the information you want. Sean [[alternative HTML version deleted]]
ADD COMMENT •
0
Entering edit mode
On Thu, Aug 20, 2009 at 3:31 PM, Sean Davis<seandavi at="" gmail.com=""> wrote: > > > On Thu, Aug 20, 2009 at 4:24 PM, Peng Yu <pengyu.ut at="" gmail.com=""> wrote: >> >> Hi, >> >> I run the following command. But it only gives the file names. I am >> wondering if there is a way to get the filename along with the >> directory name, i.e., 'data/ki10923.CEL', etc. >> >> Regards, >> Peng >> >> > list.celfiles('data/') >> ?[1] "ki10923.CEL" "ki10924.CEL" "ki10925.CEL" "ki10926.CEL" "ki10928.CEL" >> ?[6] "wt10921.CEL" "wt10922.CEL" "wt10927.CEL" "wt10930.CEL" "wt10980.CEL" > > Hi, Peng. > > Reading the help for list.celfiles(), it suggests that all arguments are > passed along to the list.files().? Reading the help for list.files() > suggests that including full.names=TRUE will return the information you > want. > > Sean > > I have checked the help page before I sent the message. But the help page that I got did not show much information. See below the email. My sessionInfo is shown below the help page. Is my documentation outdated? I remember that my R installation was updated only two weeks ago. Regards, Peng list.celfiles package:oligo R Documentation List CEL/XYS files Description: Lists the CEL/XYS files. Usage: list.celfiles(...) Arguments: Value: Character vector with the filenames. Examples: list.xysfiles() list.celfiles() > sessionInfo() R version 2.9.1 (2009-06-26) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] oligo_1.8.1 preprocessCore_1.6.0 oligoClasses_1.6.0 [4] Biobase_2.4.1 loaded via a namespace (and not attached): [1] affxparser_1.16.0 affyio_1.12.0 Biostrings_2.12.8 DBI_0.2-4 [5] IRanges_1.2.3 splines_2.9.1
ADD REPLY •
0
Entering edit mode
Peng, the part that was omitted in your message was: Arguments: ...: parameters to be passed to 'list.files' and note my sessionInfo() (it's a very old R 2.9.x that I'm running, but it doesn't play a role in this case). b > sessionInfo() R version 2.9.0 RC (2009-04-10 r48321) x86_64-unknown-linux-gnu locale: LC_CTYPE = en_US .iso885915 ;LC_NUMERIC = C ;LC_TIME = en_US .iso885915 ;LC_COLLATE = en_US .iso885915 ;LC_MONETARY = C ;LC_MESSAGES = en_US .iso885915 ;LC_PAPER = en_US .iso885915 ;LC_NAME = C ;LC_ADDRESS =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.iso885915;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] oligo_1.8.1 preprocessCore_1.6.0 oligoClasses_1.6.0 [4] Biobase_2.4.1 loaded via a namespace (and not attached): [1] affxparser_1.17.2 affyio_1.12.0 Biostrings_2.11.52 DBI_0.2-4 [5] IRanges_1.1.66 splines_2.9.0 On Aug 20, 2009, at 6:10 PM, Peng Yu wrote: > On Thu, Aug 20, 2009 at 3:31 PM, Sean Davis<seandavi at="" gmail.com=""> wrote: >> >> >> On Thu, Aug 20, 2009 at 4:24 PM, Peng Yu <pengyu.ut at="" gmail.com=""> wrote: >>> >>> Hi, >>> >>> I run the following command. But it only gives the file names. I am >>> wondering if there is a way to get the filename along with the >>> directory name, i.e., 'data/ki10923.CEL', etc. >>> >>> Regards, >>> Peng >>> >>>> list.celfiles('data/') >>> [1] "ki10923.CEL" "ki10924.CEL" "ki10925.CEL" "ki10926.CEL" >>> "ki10928.CEL" >>> [6] "wt10921.CEL" "wt10922.CEL" "wt10927.CEL" "wt10930.CEL" >>> "wt10980.CEL" >> >> Hi, Peng. >> >> Reading the help for list.celfiles(), it suggests that all >> arguments are >> passed along to the list.files(). Reading the help for list.files() >> suggests that including full.names=TRUE will return the information >> you >> want. >> >> Sean >> >> > > I have checked the help page before I sent the message. But the help > page that I got did not show much information. See below the email. My > sessionInfo is shown below the help page. Is my documentation > outdated? I remember that my R installation was updated only two weeks > ago. > > Regards, > Peng > > list.celfiles package:oligo R Documentation > > List CEL/XYS files > > Description: > > Lists the CEL/XYS files. > > Usage: > > list.celfiles(...) > > Arguments: > > > > Value: > > Character vector with the filenames. > > Examples: > > list.xysfiles() > list.celfiles() > > > >> sessionInfo() > R version 2.9.1 (2009-06-26) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE > = > en_US > .UTF > -8 > ;LC_NUMERIC > = > C > ;LC_TIME > = > en_US > .UTF > -8 > ;LC_COLLATE > = > en_US > .UTF > -8 > ;LC_MONETARY > = > C > ;LC_MESSAGES > = > en_US > .UTF > -8 > ;LC_PAPER > = > en_US > .UTF > -8 > ;LC_NAME > = > C > ;LC_ADDRESS > =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] oligo_1.8.1 preprocessCore_1.6.0 oligoClasses_1.6.0 > [4] Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] affxparser_1.16.0 affyio_1.12.0 Biostrings_2.12.8 DBI_0.2-4 > [5] IRanges_1.2.3 splines_2.9.1 > > _______________________________________________ > 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
ADD REPLY •
0
Entering edit mode
Hi, So in summary, you use an older version of R than mine, but you get a newer version of help page. This is really strange. Can somebody help me figure out what the problem is with my R installation? Regards, Peng On Thu, Aug 20, 2009 at 4:51 PM, Benilton Carvalho<bcarvalh at="" jhsph.edu=""> wrote: > Peng, > > the part that was omitted in your message was: > > Arguments: > > ? ? ...: parameters to be passed to 'list.files' > > and note my sessionInfo() (it's a very old R 2.9.x that I'm running, but it > doesn't play a role in this case). > > b > >> sessionInfo() > R version 2.9.0 RC (2009-04-10 r48321) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.iso885915;LC_NUMERIC=C;LC_TIME=en_US.iso885915;LC_COL LATE=en_US.iso885915;LC_MONETARY=C;LC_MESSAGES=en_US.iso885915;LC_PAPE R=en_US.iso885915;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT =en_US.iso885915;LC_IDENTIFICATION=C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] oligo_1.8.1 ? ? ? ? ?preprocessCore_1.6.0 oligoClasses_1.6.0 > [4] Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] affxparser_1.17.2 ?affyio_1.12.0 ? ? ?Biostrings_2.11.52 DBI_0.2-4 > [5] IRanges_1.1.66 ? ? splines_2.9.0 > > > On Aug 20, 2009, at 6:10 PM, Peng Yu wrote: > >> On Thu, Aug 20, 2009 at 3:31 PM, Sean Davis<seandavi at="" gmail.com=""> wrote: >>> >>> >>> On Thu, Aug 20, 2009 at 4:24 PM, Peng Yu <pengyu.ut at="" gmail.com=""> wrote: >>>> >>>> Hi, >>>> >>>> I run the following command. But it only gives the file names. I am >>>> wondering if there is a way to get the filename along with the >>>> directory name, i.e., 'data/ki10923.CEL', etc. >>>> >>>> Regards, >>>> Peng >>>> >>>>> list.celfiles('data/') >>>> >>>> [1] "ki10923.CEL" "ki10924.CEL" "ki10925.CEL" "ki10926.CEL" >>>> "ki10928.CEL" >>>> [6] "wt10921.CEL" "wt10922.CEL" "wt10927.CEL" "wt10930.CEL" >>>> "wt10980.CEL" >>> >>> Hi, Peng. >>> >>> Reading the help for list.celfiles(), it suggests that all arguments are >>> passed along to the list.files(). ?Reading the help for list.files() >>> suggests that including full.names=TRUE will return the information you >>> want. >>> >>> Sean >>> >>> >> >> I have checked the help page before I sent the message. But the help >> page that I got did not show much information. See below the email. My >> sessionInfo is shown below the help page. Is my documentation >> outdated? I remember that my R installation was updated only two weeks >> ago. >> >> Regards, >> Peng >> >> list.celfiles ? ? ? ? ? ? package:oligo ? ? ? ? ? ? R Documentation >> >> List CEL/XYS files >> >> Description: >> >> ? ?Lists the CEL/XYS files. >> >> Usage: >> >> ? ?list.celfiles(...) >> >> Arguments: >> >> >> >> Value: >> >> ? ?Character vector with the filenames. >> >> Examples: >> >> ? ?list.xysfiles() >> ? ?list.celfiles() >> >> >> >>> sessionInfo() >> >> R version 2.9.1 (2009-06-26) >> x86_64-unknown-linux-gnu >> >> locale: >> >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=C >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] oligo_1.8.1 ? ? ? ? ?preprocessCore_1.6.0 oligoClasses_1.6.0 >> [4] Biobase_2.4.1 >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.16.0 affyio_1.12.0 ? ? Biostrings_2.12.8 DBI_0.2-4 >> [5] IRanges_1.2.3 ? ? splines_2.9.1 >> >> _______________________________________________ >> 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 > >
ADD REPLY •
0
Entering edit mode
Hi Peng, That's not what I meant. My point was that my oligo version is the same as yours. Therefore, the documentation must be the same. And mine describes the use of "..." (dots). b On Aug 20, 2009, at 8:43 PM, Peng Yu wrote: > Hi, > > So in summary, you use an older version of R than mine, but you get a > newer version of help page. This is really strange. Can somebody help > me figure out what the problem is with my R installation? > > Regards, > Peng > > On Thu, Aug 20, 2009 at 4:51 PM, Benilton > Carvalho<bcarvalh at="" jhsph.edu=""> wrote: >> Peng, >> >> the part that was omitted in your message was: >> >> Arguments: >> >> ...: parameters to be passed to 'list.files' >> >> and note my sessionInfo() (it's a very old R 2.9.x that I'm >> running, but it >> doesn't play a role in this case). >> >> b >> >>> sessionInfo() >> R version 2.9.0 RC (2009-04-10 r48321) >> x86_64-unknown-linux-gnu >> >> locale: >> LC_CTYPE >> = >> en_US >> .iso885915 >> ;LC_NUMERIC >> = >> C >> ;LC_TIME >> = >> en_US >> .iso885915 >> ;LC_COLLATE >> = >> en_US >> .iso885915 >> ;LC_MONETARY >> = >> C >> ;LC_MESSAGES >> = >> en_US >> .iso885915 >> ;LC_PAPER >> = >> en_US >> .iso885915 >> ;LC_NAME >> = >> C >> ;LC_ADDRESS >> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.iso885915;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] oligo_1.8.1 preprocessCore_1.6.0 oligoClasses_1.6.0 >> [4] Biobase_2.4.1 >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.17.2 affyio_1.12.0 Biostrings_2.11.52 >> DBI_0.2-4 >> [5] IRanges_1.1.66 splines_2.9.0 >> >> >> On Aug 20, 2009, at 6:10 PM, Peng Yu wrote: >> >>> On Thu, Aug 20, 2009 at 3:31 PM, Sean Davis<seandavi at="" gmail.com=""> >>> wrote: >>>> >>>> >>>> On Thu, Aug 20, 2009 at 4:24 PM, Peng Yu <pengyu.ut at="" gmail.com=""> >>>> wrote: >>>>> >>>>> Hi, >>>>> >>>>> I run the following command. But it only gives the file names. I >>>>> am >>>>> wondering if there is a way to get the filename along with the >>>>> directory name, i.e., 'data/ki10923.CEL', etc. >>>>> >>>>> Regards, >>>>> Peng >>>>> >>>>>> list.celfiles('data/') >>>>> >>>>> [1] "ki10923.CEL" "ki10924.CEL" "ki10925.CEL" "ki10926.CEL" >>>>> "ki10928.CEL" >>>>> [6] "wt10921.CEL" "wt10922.CEL" "wt10927.CEL" "wt10930.CEL" >>>>> "wt10980.CEL" >>>> >>>> Hi, Peng. >>>> >>>> Reading the help for list.celfiles(), it suggests that all >>>> arguments are >>>> passed along to the list.files(). Reading the help for >>>> list.files() >>>> suggests that including full.names=TRUE will return the >>>> information you >>>> want. >>>> >>>> Sean >>>> >>>> >>> >>> I have checked the help page before I sent the message. But the help >>> page that I got did not show much information. See below the >>> email. My >>> sessionInfo is shown below the help page. Is my documentation >>> outdated? I remember that my R installation was updated only two >>> weeks >>> ago. >>> >>> Regards, >>> Peng >>> >>> list.celfiles package:oligo R Documentation >>> >>> List CEL/XYS files >>> >>> Description: >>> >>> Lists the CEL/XYS files. >>> >>> Usage: >>> >>> list.celfiles(...) >>> >>> Arguments: >>> >>> >>> >>> Value: >>> >>> Character vector with the filenames. >>> >>> Examples: >>> >>> list.xysfiles() >>> list.celfiles() >>> >>> >>> >>>> sessionInfo() >>> >>> R version 2.9.1 (2009-06-26) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> >>> LC_CTYPE >>> = >>> en_US >>> .UTF >>> -8 >>> ;LC_NUMERIC >>> = >>> C >>> ;LC_TIME >>> = >>> en_US >>> .UTF >>> -8 >>> ;LC_COLLATE >>> = >>> en_US >>> .UTF >>> -8 >>> ;LC_MONETARY >>> = >>> C >>> ;LC_MESSAGES >>> = >>> en_US >>> .UTF >>> -8 >>> ;LC_PAPER >>> = >>> en_US >>> .UTF >>> -8 >>> ;LC_NAME >>> = >>> C >>> ;LC_ADDRESS >>> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] oligo_1.8.1 preprocessCore_1.6.0 oligoClasses_1.6.0 >>> [4] Biobase_2.4.1 >>> >>> loaded via a namespace (and not attached): >>> [1] affxparser_1.16.0 affyio_1.12.0 Biostrings_2.12.8 DBI_0.2-4 >>> [5] IRanges_1.2.3 splines_2.9.1 >>> >>> _______________________________________________ >>> 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 >> >> > > _______________________________________________ > 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
ADD REPLY •
0
Entering edit mode
I see. So we have the same version of oligo installed. But my document for oligo is less than yours. Can somebody help me on this issue? Regards, Peng On Thu, Aug 20, 2009 at 6:56 PM, Benilton Carvalho<bcarvalh at="" jhsph.edu=""> wrote: > Hi Peng, > > That's not what I meant. My point was that my oligo version is the same as > yours. Therefore, the documentation must be the same. And mine describes the > use of "..." (dots). > > b > > On Aug 20, 2009, at 8:43 PM, Peng Yu wrote: > >> Hi, >> >> So in summary, you use an older version of R than mine, but you get a >> newer version of help page. This is really strange. Can somebody help >> me figure out what the problem is with my R installation? >> >> Regards, >> Peng >> >> On Thu, Aug 20, 2009 at 4:51 PM, Benilton Carvalho<bcarvalh at="" jhsph.edu=""> >> wrote: >>> >>> Peng, >>> >>> the part that was omitted in your message was: >>> >>> Arguments: >>> >>> ? ...: parameters to be passed to 'list.files' >>> >>> and note my sessionInfo() (it's a very old R 2.9.x that I'm running, but >>> it >>> doesn't play a role in this case). >>> >>> b >>> >>>> sessionInfo() >>> >>> R version 2.9.0 RC (2009-04-10 r48321) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> >>> LC_CTYPE=en_US.iso885915;LC_NUMERIC=C;LC_TIME=en_US.iso885915;LC_C OLLATE=en_US.iso885915;LC_MONETARY=C;LC_MESSAGES=en_US.iso885915;LC_PA PER=en_US.iso885915;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREME NT=en_US.iso885915;LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>> >>> other attached packages: >>> [1] oligo_1.8.1 ? ? ? ? ?preprocessCore_1.6.0 oligoClasses_1.6.0 >>> [4] Biobase_2.4.1 >>> >>> loaded via a namespace (and not attached): >>> [1] affxparser_1.17.2 ?affyio_1.12.0 ? ? ?Biostrings_2.11.52 DBI_0.2-4 >>> [5] IRanges_1.1.66 ? ? splines_2.9.0 >>> >>> >>> On Aug 20, 2009, at 6:10 PM, Peng Yu wrote: >>> >>>> On Thu, Aug 20, 2009 at 3:31 PM, Sean Davis<seandavi at="" gmail.com=""> wrote: >>>>> >>>>> >>>>> On Thu, Aug 20, 2009 at 4:24 PM, Peng Yu <pengyu.ut at="" gmail.com=""> wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>> I run the following command. But it only gives the file names. I am >>>>>> wondering if there is a way to get the filename along with the >>>>>> directory name, i.e., 'data/ki10923.CEL', etc. >>>>>> >>>>>> Regards, >>>>>> Peng >>>>>> >>>>>>> list.celfiles('data/') >>>>>> >>>>>> [1] "ki10923.CEL" "ki10924.CEL" "ki10925.CEL" "ki10926.CEL" >>>>>> "ki10928.CEL" >>>>>> [6] "wt10921.CEL" "wt10922.CEL" "wt10927.CEL" "wt10930.CEL" >>>>>> "wt10980.CEL" >>>>> >>>>> Hi, Peng. >>>>> >>>>> Reading the help for list.celfiles(), it suggests that all arguments >>>>> are >>>>> passed along to the list.files(). ?Reading the help for list.files() >>>>> suggests that including full.names=TRUE will return the information you >>>>> want. >>>>> >>>>> Sean >>>>> >>>>> >>>> >>>> I have checked the help page before I sent the message. But the help >>>> page that I got did not show much information. See below the email. My >>>> sessionInfo is shown below the help page. Is my documentation >>>> outdated? I remember that my R installation was updated only two weeks >>>> ago. >>>> >>>> Regards, >>>> Peng >>>> >>>> list.celfiles ? ? ? ? ? ? package:oligo ? ? ? ? ? ? R Documentation >>>> >>>> List CEL/XYS files >>>> >>>> Description: >>>> >>>> ?Lists the CEL/XYS files. >>>> >>>> Usage: >>>> >>>> ?list.celfiles(...) >>>> >>>> Arguments: >>>> >>>> >>>> >>>> Value: >>>> >>>> ?Character vector with the filenames. >>>> >>>> Examples: >>>> >>>> ?list.xysfiles() >>>> ?list.celfiles() >>>> >>>> >>>> >>>>> sessionInfo() >>>> >>>> R version 2.9.1 (2009-06-26) >>>> x86_64-unknown-linux-gnu >>>> >>>> locale: >>>> >>>> >>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE= en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8 ;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_I DENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>> >>>> other attached packages: >>>> [1] oligo_1.8.1 ? ? ? ? ?preprocessCore_1.6.0 oligoClasses_1.6.0 >>>> [4] Biobase_2.4.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affxparser_1.16.0 affyio_1.12.0 ? ? Biostrings_2.12.8 DBI_0.2-4 >>>> [5] IRanges_1.2.3 ? ? splines_2.9.1 >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> >> _______________________________________________ >> 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 > >
ADD REPLY •
0
Entering edit mode
reinstall it... as a bonus, you'll get a slightly newer version. source("http://www.bioconductor.org/biocLite.R") biocLite("oligo") On Aug 20, 2009, at 9:11 PM, Peng Yu wrote: > I see. So we have the same version of oligo installed. But my document > for oligo is less than yours. Can somebody help me on this issue? > > Regards, > Peng > > On Thu, Aug 20, 2009 at 6:56 PM, Benilton > Carvalho<bcarvalh at="" jhsph.edu=""> wrote: >> Hi Peng, >> >> That's not what I meant. My point was that my oligo version is the >> same as >> yours. Therefore, the documentation must be the same. And mine >> describes the >> use of "..." (dots). >> >> b >> >> On Aug 20, 2009, at 8:43 PM, Peng Yu wrote: >> >>> Hi, >>> >>> So in summary, you use an older version of R than mine, but you >>> get a >>> newer version of help page. This is really strange. Can somebody >>> help >>> me figure out what the problem is with my R installation? >>> >>> Regards, >>> Peng >>> >>> On Thu, Aug 20, 2009 at 4:51 PM, Benilton Carvalho<bcarvalh at="" jhsph.edu="">>> > >>> wrote: >>>> >>>> Peng, >>>> >>>> the part that was omitted in your message was: >>>> >>>> Arguments: >>>> >>>> ...: parameters to be passed to 'list.files' >>>> >>>> and note my sessionInfo() (it's a very old R 2.9.x that I'm >>>> running, but >>>> it >>>> doesn't play a role in this case). >>>> >>>> b >>>> >>>>> sessionInfo() >>>> >>>> R version 2.9.0 RC (2009-04-10 r48321) >>>> x86_64-unknown-linux-gnu >>>> >>>> locale: >>>> >>>> LC_CTYPE >>>> = >>>> en_US >>>> .iso885915 >>>> ;LC_NUMERIC >>>> = >>>> C >>>> ;LC_TIME >>>> = >>>> en_US >>>> .iso885915 >>>> ;LC_COLLATE >>>> = >>>> en_US >>>> .iso885915 >>>> ;LC_MONETARY >>>> = >>>> C >>>> ;LC_MESSAGES >>>> = >>>> en_US >>>> .iso885915 >>>> ;LC_PAPER >>>> = >>>> en_US >>>> .iso885915 >>>> ;LC_NAME >>>> = >>>> C >>>> ;LC_ADDRESS >>>> = >>>> C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.iso885915;LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods >>>> base >>>> >>>> other attached packages: >>>> [1] oligo_1.8.1 preprocessCore_1.6.0 oligoClasses_1.6.0 >>>> [4] Biobase_2.4.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affxparser_1.17.2 affyio_1.12.0 Biostrings_2.11.52 >>>> DBI_0.2-4 >>>> [5] IRanges_1.1.66 splines_2.9.0 >>>> >>>> >>>> On Aug 20, 2009, at 6:10 PM, Peng Yu wrote: >>>> >>>>> On Thu, Aug 20, 2009 at 3:31 PM, Sean Davis<seandavi at="" gmail.com=""> >>>>> wrote: >>>>>> >>>>>> >>>>>> On Thu, Aug 20, 2009 at 4:24 PM, Peng Yu <pengyu.ut at="" gmail.com=""> >>>>>> wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I run the following command. But it only gives the file names. >>>>>>> I am >>>>>>> wondering if there is a way to get the filename along with the >>>>>>> directory name, i.e., 'data/ki10923.CEL', etc. >>>>>>> >>>>>>> Regards, >>>>>>> Peng >>>>>>> >>>>>>>> list.celfiles('data/') >>>>>>> >>>>>>> [1] "ki10923.CEL" "ki10924.CEL" "ki10925.CEL" "ki10926.CEL" >>>>>>> "ki10928.CEL" >>>>>>> [6] "wt10921.CEL" "wt10922.CEL" "wt10927.CEL" "wt10930.CEL" >>>>>>> "wt10980.CEL" >>>>>> >>>>>> Hi, Peng. >>>>>> >>>>>> Reading the help for list.celfiles(), it suggests that all >>>>>> arguments >>>>>> are >>>>>> passed along to the list.files(). Reading the help for >>>>>> list.files() >>>>>> suggests that including full.names=TRUE will return the >>>>>> information you >>>>>> want. >>>>>> >>>>>> Sean >>>>>> >>>>>> >>>>> >>>>> I have checked the help page before I sent the message. But the >>>>> help >>>>> page that I got did not show much information. See below the >>>>> email. My >>>>> sessionInfo is shown below the help page. Is my documentation >>>>> outdated? I remember that my R installation was updated only two >>>>> weeks >>>>> ago. >>>>> >>>>> Regards, >>>>> Peng >>>>> >>>>> list.celfiles package:oligo R >>>>> Documentation >>>>> >>>>> List CEL/XYS files >>>>> >>>>> Description: >>>>> >>>>> Lists the CEL/XYS files. >>>>> >>>>> Usage: >>>>> >>>>> list.celfiles(...) >>>>> >>>>> Arguments: >>>>> >>>>> >>>>> >>>>> Value: >>>>> >>>>> Character vector with the filenames. >>>>> >>>>> Examples: >>>>> >>>>> list.xysfiles() >>>>> list.celfiles() >>>>> >>>>> >>>>> >>>>>> sessionInfo() >>>>> >>>>> R version 2.9.1 (2009-06-26) >>>>> x86_64-unknown-linux-gnu >>>>> >>>>> locale: >>>>> >>>>> >>>>> LC_CTYPE >>>>> = >>>>> en_US >>>>> .UTF >>>>> -8 >>>>> ;LC_NUMERIC >>>>> = >>>>> C >>>>> ;LC_TIME >>>>> = >>>>> en_US >>>>> .UTF >>>>> -8 >>>>> ;LC_COLLATE >>>>> = >>>>> en_US >>>>> .UTF >>>>> -8 >>>>> ;LC_MONETARY >>>>> = >>>>> C >>>>> ;LC_MESSAGES >>>>> = >>>>> en_US >>>>> .UTF >>>>> -8 >>>>> ;LC_PAPER >>>>> = >>>>> en_US >>>>> .UTF >>>>> -8 >>>>> ;LC_NAME >>>>> = >>>>> C >>>>> ;LC_ADDRESS >>>>> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods >>>>> base >>>>> >>>>> other attached packages: >>>>> [1] oligo_1.8.1 preprocessCore_1.6.0 oligoClasses_1.6.0 >>>>> [4] Biobase_2.4.1 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] affxparser_1.16.0 affyio_1.12.0 Biostrings_2.12.8 >>>>> DBI_0.2-4 >>>>> [5] IRanges_1.2.3 splines_2.9.1 >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>> >>> _______________________________________________ >>> 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 >> >> > > _______________________________________________ > 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
ADD REPLY •
0
Entering edit mode
On Thu, Aug 20, 2009 at 7:43 PM, Peng Yu <pengyu.ut@gmail.com> wrote: > Hi, > > So in summary, you use an older version of R than mine, but you get a > newer version of help page. This is really strange. Can somebody help > me figure out what the problem is with my R installation? > Hi, Peng. You'll want to look at the section called "Arguments" in the help file. That is where the suggestion to look at list.files() comes. I do not think there is a problem with your installation, at least not contributing to the current problem. Sean > n Thu, Aug 20, 2009 at 4:51 PM, Benilton Carvalho<bcarvalh@jhsph.edu> > wrote: > > Peng, > > > > the part that was omitted in your message was: > > > > Arguments: > > > > ...: parameters to be passed to 'list.files' > > > > and note my sessionInfo() (it's a very old R 2.9.x that I'm running, but > it > > doesn't play a role in this case). > > > > b > > > >> sessionInfo() > > R version 2.9.0 RC (2009-04-10 r48321) > > x86_64-unknown-linux-gnu > > > > locale: > > > LC_CTYPE=en_US.iso885915;LC_NUMERIC=C;LC_TIME=en_US.iso885915;LC_COL LATE=en_US.iso885915;LC_MONETARY=C;LC_MESSAGES=en_US.iso885915;LC_PAPE R=en_US.iso885915;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT =en_US.iso885915;LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] oligo_1.8.1 preprocessCore_1.6.0 oligoClasses_1.6.0 > > [4] Biobase_2.4.1 > > > > loaded via a namespace (and not attached): > > [1] affxparser_1.17.2 affyio_1.12.0 Biostrings_2.11.52 DBI_0.2-4 > > [5] IRanges_1.1.66 splines_2.9.0 > > > > > > On Aug 20, 2009, at 6:10 PM, Peng Yu wrote: > > > >> On Thu, Aug 20, 2009 at 3:31 PM, Sean Davis<seandavi@gmail.com> wrote: > >>> > >>> > >>> On Thu, Aug 20, 2009 at 4:24 PM, Peng Yu <pengyu.ut@gmail.com> wrote: > >>>> > >>>> Hi, > >>>> > >>>> I run the following command. But it only gives the file names. I am > >>>> wondering if there is a way to get the filename along with the > >>>> directory name, i.e., 'data/ki10923.CEL', etc. > >>>> > >>>> Regards, > >>>> Peng > >>>> > >>>>> list.celfiles('data/') > >>>> > >>>> [1] "ki10923.CEL" "ki10924.CEL" "ki10925.CEL" "ki10926.CEL" > >>>> "ki10928.CEL" > >>>> [6] "wt10921.CEL" "wt10922.CEL" "wt10927.CEL" "wt10930.CEL" > >>>> "wt10980.CEL" > >>> > >>> Hi, Peng. > >>> > >>> Reading the help for list.celfiles(), it suggests that all arguments > are > >>> passed along to the list.files(). Reading the help for list.files() > >>> suggests that including full.names=TRUE will return the information you > >>> want. > >>> > >>> Sean > >>> > >>> > >> > >> I have checked the help page before I sent the message. But the help > >> page that I got did not show much information. See below the email. My > >> sessionInfo is shown below the help page. Is my documentation > >> outdated? I remember that my R installation was updated only two weeks > >> ago. > >> > >> Regards, > >> Peng > >> > >> list.celfiles package:oligo R Documentation > >> > >> List CEL/XYS files > >> > >> Description: > >> > >> Lists the CEL/XYS files. > >> > >> Usage: > >> > >> list.celfiles(...) > >> > >> Arguments: > >> > >> > >> > >> Value: > >> > >> Character vector with the filenames. > >> > >> Examples: > >> > >> list.xysfiles() > >> list.celfiles() > >> > >> > >> > >>> sessionInfo() > >> > >> R version 2.9.1 (2009-06-26) > >> x86_64-unknown-linux-gnu > >> > >> locale: > >> > >> > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > >> > >> attached base packages: > >> [1] stats graphics grDevices utils datasets methods base > >> > >> other attached packages: > >> [1] oligo_1.8.1 preprocessCore_1.6.0 oligoClasses_1.6.0 > >> [4] Biobase_2.4.1 > >> > >> loaded via a namespace (and not attached): > >> [1] affxparser_1.16.0 affyio_1.12.0 Biostrings_2.12.8 DBI_0.2-4 > >> [5] IRanges_1.2.3 splines_2.9.1 > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLY •
0
Entering edit mode
On Thu, Aug 20, 2009 at 7:57 PM, Sean Davis<seandavi at="" gmail.com=""> wrote: > > > On Thu, Aug 20, 2009 at 7:43 PM, Peng Yu <pengyu.ut at="" gmail.com=""> wrote: >> >> Hi, >> >> So in summary, you use an older version of R than mine, but you get a >> newer version of help page. This is really strange. Can somebody help >> me figure out what the problem is with my R installation? > > Hi, Peng.? You'll want to look at the section called "Arguments" in the help > file.? That is where the suggestion to look at list.files() comes.? I do not > think there is a problem with your installation, at least not contributing > to the current problem. I misunderstood the previous messages. Thank you for reminding me. But I think the document for list.celfiles should definitely be improved in future release of oligo. Regards, Peng
ADD REPLY •
0
Entering edit mode
Documentation is on the works, Peng. Thanks for the reminder. About list.celfiles() specifically, what is your recommendation to improve the documentation? b On Aug 20, 2009, at 10:13 PM, Peng Yu wrote: > On Thu, Aug 20, 2009 at 7:57 PM, Sean Davis<seandavi at="" gmail.com=""> wrote: >> >> >> On Thu, Aug 20, 2009 at 7:43 PM, Peng Yu <pengyu.ut at="" gmail.com=""> wrote: >>> >>> Hi, >>> >>> So in summary, you use an older version of R than mine, but you >>> get a >>> newer version of help page. This is really strange. Can somebody >>> help >>> me figure out what the problem is with my R installation? >> >> Hi, Peng. You'll want to look at the section called "Arguments" in >> the help >> file. That is where the suggestion to look at list.files() comes. >> I do not >> think there is a problem with your installation, at least not >> contributing >> to the current problem. > > I misunderstood the previous messages. Thank you for reminding me. But > I think the document for list.celfiles should definitely be improved > in future release of oligo. > > Regards, > Peng > > _______________________________________________ > 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
ADD REPLY •
0
Entering edit mode
According the previous messages in this thread, list.celfiles() forwards the arguments to list.files(). So all the arguments that accepted by list.files() should be documented in list.celfiles(). Regards, Peng On Thu, Aug 20, 2009 at 8:27 PM, Benilton Carvalho<bcarvalh at="" jhsph.edu=""> wrote: > Documentation is on the works, Peng. Thanks for the reminder. > > About list.celfiles() specifically, what is your recommendation to improve > the documentation? > > b > > On Aug 20, 2009, at 10:13 PM, Peng Yu wrote: > >> On Thu, Aug 20, 2009 at 7:57 PM, Sean Davis<seandavi at="" gmail.com=""> wrote: >>> >>> >>> On Thu, Aug 20, 2009 at 7:43 PM, Peng Yu <pengyu.ut at="" gmail.com=""> wrote: >>>> >>>> Hi, >>>> >>>> So in summary, you use an older version of R than mine, but you get a >>>> newer version of help page. This is really strange. Can somebody help >>>> me figure out what the problem is with my R installation? >>> >>> Hi, Peng. ?You'll want to look at the section called "Arguments" in the >>> help >>> file. ?That is where the suggestion to look at list.files() comes. ?I do >>> not >>> think there is a problem with your installation, at least not >>> contributing >>> to the current problem. >> >> I misunderstood the previous messages. Thank you for reminding me. But >> I think the document for list.celfiles should definitely be improved >> in future release of oligo. >> >> Regards, >> Peng >> >> _______________________________________________ >> 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 > >
ADD REPLY •
0
Entering edit mode
Just added some more details to the documentation of that function, which will appear in the devel branch, say, in 2 days. Those won't save you from reading the help page for list.files() though (as already documented). b On Aug 20, 2009, at 10:59 PM, Peng Yu wrote: > According the previous messages in this thread, list.celfiles() > forwards the arguments to list.files(). So all the arguments that > accepted by list.files() should be documented in list.celfiles(). > > Regards, > Peng > > On Thu, Aug 20, 2009 at 8:27 PM, Benilton > Carvalho<bcarvalh at="" jhsph.edu=""> wrote: >> Documentation is on the works, Peng. Thanks for the reminder. >> >> About list.celfiles() specifically, what is your recommendation to >> improve >> the documentation? >> >> b >> >> On Aug 20, 2009, at 10:13 PM, Peng Yu wrote: >> >>> On Thu, Aug 20, 2009 at 7:57 PM, Sean Davis<seandavi at="" gmail.com=""> >>> wrote: >>>> >>>> >>>> On Thu, Aug 20, 2009 at 7:43 PM, Peng Yu <pengyu.ut at="" gmail.com=""> >>>> wrote: >>>>> >>>>> Hi, >>>>> >>>>> So in summary, you use an older version of R than mine, but you >>>>> get a >>>>> newer version of help page. This is really strange. Can somebody >>>>> help >>>>> me figure out what the problem is with my R installation? >>>> >>>> Hi, Peng. You'll want to look at the section called "Arguments" >>>> in the >>>> help >>>> file. That is where the suggestion to look at list.files() >>>> comes. I do >>>> not >>>> think there is a problem with your installation, at least not >>>> contributing >>>> to the current problem. >>> >>> I misunderstood the previous messages. Thank you for reminding me. >>> But >>> I think the document for list.celfiles should definitely be improved >>> in future release of oligo. >>> >>> Regards, >>> Peng >>> >>> _______________________________________________ >>> 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 >> >> > > _______________________________________________ > 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
ADD REPLY •
0
Entering edit mode
On Fri, Aug 21, 2009 at 3:59 AM, Peng Yu<pengyu.ut at="" gmail.com=""> wrote: > According the previous messages in this thread, list.celfiles() > forwards the arguments to list.files(). So all the arguments that > accepted by list.files() should be documented in list.celfiles(). A common strategy among package developers is to *minimize the redundancy* of code and documentation in order to improve quality and ease maintenance. By passing down arguments to internal/support functions via '...', and not replicating the argument names and pass then explicitly (e.g. full.names=full.names), you will always get access to the most up-to-date features *and* documentation of the internal function (here list.files()) in case that is updated. Vice versa, if list.files() is updated with, say, new arguments the list.celfiles() and oligo does not have to be updated. This means that you as a user don't have to wait for a package to be updated and the package developer don't have to keep track of all updates occurring in all other packages. Maintaining package code and documentation is already time consuming as it is. So, if I was the developer of oligo, I would (for my and the user's sake) *not* document list.files() argument explicitly in list.celfiles() beyond "{...}{Additional arguments passed to list.files().}. My $.02 /Henrik > > Regards, > Peng > > On Thu, Aug 20, 2009 at 8:27 PM, Benilton Carvalho<bcarvalh at="" jhsph.edu=""> wrote: >> Documentation is on the works, Peng. Thanks for the reminder. >> >> About list.celfiles() specifically, what is your recommendation to improve >> the documentation? >> >> b >> >> On Aug 20, 2009, at 10:13 PM, Peng Yu wrote: >> >>> On Thu, Aug 20, 2009 at 7:57 PM, Sean Davis<seandavi at="" gmail.com=""> wrote: >>>> >>>> >>>> On Thu, Aug 20, 2009 at 7:43 PM, Peng Yu <pengyu.ut at="" gmail.com=""> wrote: >>>>> >>>>> Hi, >>>>> >>>>> So in summary, you use an older version of R than mine, but you get a >>>>> newer version of help page. This is really strange. Can somebody help >>>>> me figure out what the problem is with my R installation? >>>> >>>> Hi, Peng. ?You'll want to look at the section called "Arguments" in the >>>> help >>>> file. ?That is where the suggestion to look at list.files() comes. ?I do >>>> not >>>> think there is a problem with your installation, at least not >>>> contributing >>>> to the current problem. >>> >>> I misunderstood the previous messages. Thank you for reminding me. But >>> I think the document for list.celfiles should definitely be improved >>> in future release of oligo. >>> >>> Regards, >>> Peng >>> >>> _______________________________________________ >>> 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 >> >> > > _______________________________________________ > 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 >
ADD REPLY •
0
Entering edit mode
Henrik Bengtsson wrote: > A common strategy among package developers is to *minimize the > redundancy* of code and documentation in order to improve quality and > ease maintenance. > I agree with Henrik here, especially the point about minimizing redundancy. It is not a big deal to go from ?list.celfiles to ?list.files. Saroj > My $.02 > > /Henrik > > > >> Regards, >> Peng >> >> On Thu, Aug 20, 2009 at 8:27 PM, Benilton Carvalho<bcarvalh at="" jhsph.edu=""> wrote: >> >>> Documentation is on the works, Peng. Thanks for the reminder. >>> >>> About list.celfiles() specifically, what is your recommendation to improve >>> the documentation? >>> >>> b >>> >>> On Aug 20, 2009, at 10:13 PM, Peng Yu wrote: >>> >>> >>>> On Thu, Aug 20, 2009 at 7:57 PM, Sean Davis<seandavi at="" gmail.com=""> wrote: >>>> >>>>> On Thu, Aug 20, 2009 at 7:43 PM, Peng Yu <pengyu.ut at="" gmail.com=""> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> So in summary, you use an older version of R than mine, but you get a >>>>>> newer version of help page. This is really strange. Can somebody help >>>>>> me figure out what the problem is with my R installation? >>>>>> >>>>> Hi, Peng. You'll want to look at the section called "Arguments" in the >>>>> help >>>>> file. That is where the suggestion to look at list.files() comes. I do >>>>> not >>>>> think there is a problem with your installation, at least not >>>>> contributing >>>>> to the current problem. >>>>> >>>> I misunderstood the previous messages. Thank you for reminding me. But >>>> I think the document for list.celfiles should definitely be improved >>>> in future release of oligo. >>>> >>>> Regards, >>>> Peng >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >> _______________________________________________ >> 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 >> >> > > _______________________________________________ > 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 > >
ADD REPLY •
0
Entering edit mode
@steve-lianoglou-2771
Last seen 22 months ago
United States
Hi, On Aug 20, 2009, at 4:24 PM, Peng Yu wrote: > Hi, > > I run the following command. But it only gives the file names. I am > wondering if there is a way to get the filename along with the > directory name, i.e., 'data/ki10923.CEL', etc. > > Regards, > Peng > >> list.celfiles('data/') > [1] "ki10923.CEL" "ki10924.CEL" "ki10925.CEL" "ki10926.CEL" > "ki10928.CEL" > [6] "wt10921.CEL" "wt10922.CEL" "wt10927.CEL" "wt10930.CEL" > "wt10980.CEL" Look at the help for list.celfiles (or its source): it sends all of its args to the list.files function In ?list.files you'll find that you just have to set full.names=TRUE -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD COMMENT •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 702 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6