Hi!I'm doing a little data importing from .cel files,> setwd("/home/mandova/celfiles") > mydata<-ReadAffy()Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) : unused argument(s) (extended = TRUE) Then I tried> filenames<-paste("GSM",c(seq(138597,138617,1)),".cel",sep="")> filenames<-as.character(filenames)> filenames[1] "GSM138597.cel" "GSM138598.cel" "GSM138599.cel" "GSM138600.cel" [5] "GSM138601.cel" "GSM138602.cel" "GSM138603.cel" "GSM138604.cel" [9] "GSM138605.cel" "GSM138606.cel" "GSM138607.cel" "GSM138608.cel" [13] "GSM138609.cel" "GSM138610.cel" "GSM138611.cel" "GSM138612.cel" [17] "GSM138613.cel" "GSM138614.cel" "GSM138615.cel" "GSM138616.cel" [21] "GSM138617.cel"> mydata<-ReadAffy(compress=FALSE,filenames=filenames)Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) : unused argument(s) (extended = TRUE) Same error! Could you please help me understand the error message? Thx!!! -- View this message in context: http://r.789695.n4.nabble.com/error-with-ReadAffy-tp2313415p2313415.html Sent from the R help mailing list archive at Nabble.com.
I don't know if it has anything to do with these installation warnings:
* installing to library ?/home/mandova/R/i486-pc-linux-gnu-library/2.11?
* installing *source* package ?affy? ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1 -fpic -g -O2 -c
chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1 -fpic -g -O2 -c
getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1 -fpic -g -O2 -c
mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1 -fpic -g -O2 -c
qnorm.c -o qnorm.o
gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1 -fpic -g -O2 -c
rma2.c -o rma2.o
rma2.c: In function ?rma_c_call?:
rma2.c:499: warning: assignment discards qualifiers from pointer target type
gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1 -fpic -g -O2 -c
rma_background2.c -o rma_background2.o
gcc -std=gnu99 -I/usr/share/R/include -DHAVE_ZLIB=1 -fpic -g -O2 -c
rma_common.c -o rma_common.o
gcc -std=gnu99 -shared -o affy.so chipbackground.o getall_locations.o
mas5calls.o qnorm.o rma2.o rma_background2.o rma_common.o -lz
-L/usr/lib/R/lib -lR
installing to /home/mandova/R/i486-pc-linux-gnu-library/2.11/affy/libs
** R
** data
** demo
** inst
Warning: field 'SaveImage' is defunct: please remove it
** preparing package for lazy loading
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages
'citation(pkgname)'.
Creating a new generic function for "open" in "affy"
Creating a new generic function for "update" in "affy"
Creating a new generic function for "close" in "affy"
** help
Warning: ./man/AffyBatch-class.Rd:121: unknown macro '\item'
Warning: ./man/AffyBatch-class.Rd:124: unknown macro '\item'
Warning: ./man/AffyBatch-class.Rd:127: unknown macro '\item'
Warning: ./man/AffyBatch-class.Rd:131: unknown macro '\item'
Warning: ./man/AffyBatch-class.Rd:133: unknown macro '\item'
Warning: ./man/AffyBatch-class.Rd:135: unknown macro '\item'
Warning: ./man/AffyBatch-class.Rd:137: unknown macro '\item'
Warning: ./man/AffyBatch-class.Rd:151: unknown macro '\item'
Warning: ./man/AffyBatch-class.Rd:153: unknown macro '\item'
Warning: ./man/AffyBatch-class.Rd:155: unknown macro '\item'
Warning: ./man/AffyBatch-class.Rd:157: unknown macro '\item'
Warning: ./man/AffyBatch-class.Rd:159: unknown macro '\item'
Warning: ./man/AffyBatch-class.Rd:161: unknown macro '\item'
Warning: ./man/AffyBatch-class.Rd:162: unknown macro '\item'
Warning: ./man/AffyBatch-class.Rd:164: unknown macro '\item'
Warning: ./man/ProbeSet-class.Rd:17: unexpected '}'
Warning: ./man/SpikeIn.Rd:17: unknown macro '\it'
Warning: ./man/SpikeIn.Rd:18: unknown macro '\it'
Warning: ./man/SpikeIn.Rd:20: unknown macro '\it'
Warning: ./man/SpikeIn.Rd:24: unknown macro '\mu'
Warning: ./man/affy-options.Rd:10: unknown macro '\begin'
Warning: ./man/affy-options.Rd:11: unknown macro '\item'
Warning: ./man/affy-options.Rd:13: unknown macro '\item'
Warning: ./man/affy-options.Rd:14: unknown macro '\item'
Warning: ./man/affy-options.Rd:15: unknown macro '\item'
Warning: ./man/affy-options.Rd:16: unknown macro '\it'
Warning: ./man/affy-options.Rd:16: unknown macro '\it'
Warning: ./man/affy-options.Rd:19: unknown macro '\it'
Warning: ./man/affy-options.Rd:19: unknown macro '\it'
Warning: ./man/affy-options.Rd:20: unknown macro '\it'
Warning: ./man/affy-options.Rd:21: unknown macro '\it'
Warning: ./man/affy-options.Rd:21: unknown macro '\it'
Warning: ./man/affy-options.Rd:21: unknown macro '\it'
Warning: ./man/affy-options.Rd:21: unknown macro '\it'
Warning: ./man/affy-options.Rd:22: unknown macro '\it'
Warning: ./man/affy-options.Rd:23: unknown macro '\begin'
Warning: ./man/affy-options.Rd:24: unknown macro '\item'
Warning: ./man/affy-options.Rd:24: unknown macro '\it'
Warning: ./man/affy-options.Rd:26: unknown macro '\item'
Warning: ./man/affy-options.Rd:26: unknown macro '\it'
Warning: ./man/affy-options.Rd:29: unknown macro '\item'
Warning: ./man/affy-options.Rd:29: unknown macro '\it'
Warning: ./man/affy-options.Rd:31: unknown macro '\end'
Warning: ./man/affy-options.Rd:32: unknown macro '\end'
Warning: ./man/bgc.Rd:33: unknown macro '\begin'
Warning: ./man/bgc.Rd:34: unknown macro '\item'
Warning: ./man/bgc.Rd:35: unknown macro '\item'
Warning: ./man/bgc.Rd:37: unknown macro '\item'
Warning: ./man/bgc.Rd:39: unknown macro '\end'
Warning: ./man/fit.li.wong.Rd:8: unexpected '}'
Warning: ./man/generateExprVal.method.playerout.Rd:31: unknown macro
'\item'
Warning: ./man/maffy.normalise.Rd:22: unexpected '}'
Warning: ./man/maffy.subset.Rd:20: unexpected '}'
Warning: ./man/maffy.subset.Rd:25: unexpected '}'
Warning: ./man/mas5calls.Rd:93: unexpected '}'
Warning: ./man/multiloess.Rd:17: unexpected '}'
Warning: ./man/multiloess.Rd:22: unexpected '}'
Warning: ./man/mva.pairs.Rd:8: unexpected '}'
Warning: ./man/normalize-methods.Rd:12: unexpected '}'
Warning: ./man/normalize.invariantset.Rd:55: unexpected '}'
Warning: ./man/normalize.qspline.Rd:79: unknown macro '\o'
Warning: ./man/normalize.qspline.Rd:80: unknown macro '\o'
Warning: ./man/plotLocation.Rd:21: unexpected '}'
Warning: ./man/setAffyOptions.Rd:19: unexpected '}'
Warning: ./man/simplemultiLoess.Rd:19: unexpected '}'
Warning: ./man/tukey.biweight.Rd:25: unexpected '}'
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (affy)
--
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