I tried to fetch and parse the GSE94 series from GEO using GEOquery library (gse<-getGEO('GSE94')). Operation is aborted with the message: Error in make.names(as.character(names), allow_) : invalid multibyte string 29 In addition: There were 12 warnings (use warnings() to see them) is that an error of getGEO or a problem of the data set? Tobias > sessionInfo() R version 2.5.1 (2007-06-27) i386-apple-darwin8.9.1 locale: en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: GEOquery "2.0.6" ====================================================================== Dr. Tobias Straub Adolf-Butenandt-Institute, Molecular Biology tel: +49-89-2180 75 439 Schillerstr. 44, 80336 Munich, Germany

Hi Tobias -- Very clever fix! I think the problem would also be solved by setting your 'locale' to a non-UTF-8., e.g., > Sys.setlocale(locale="C") (you can revert to previous settings with locale="en_US.UTF-8") I think also that there is a little mis-match between how clever R is about locales, and how clever developers like us are about locales -- I would recommend, at least at the current moment in time, setting the locale to "C" unless UTF-8 encoding is needed. Martin Tobias Straub <tstraub at="" med.uni-muenchen.de=""> writes: > ok, I figured it out myself! modified GEOquery > > *** GEOquery Fri Aug 10 08:24:53 2007 > --- GEOquery_new Fri Aug 31 14:43:15 2007 > *************** > *** 495,500 **** > --- 495,501 ---- > nextEntity <- "" > while(!finished) { > line <- readLines(con,1) > + line <- iconv(line, "LATIN2", "UTF-8") > if(length(line)==0) finished <- TRUE > a[lines] <- line > lines <- lines+1 > *************** > *** 510,515 **** > --- 511,517 ---- > finished <- FALSE > while(!finished) { > line <- readLines(con,1) > + line <- iconv(line, "LATIN2", "UTF-8") > if(length(line)==0) { > finished <- TRUE > } else { > > > On Aug 31, 2007, at 2:17 PM, Tobias Straub wrote: > >> I tried to fetch and parse the GSE94 series from GEO using GEOquery >> library (gse<-getGEO('GSE94')). Operation is aborted with the message: >> >> Error in make.names(as.character(names), allow_) : >> invalid multibyte string 29 >> In addition: There were 12 warnings (use warnings() to see them) >> >> is that an error of getGEO or a problem of the data set? >> >> Tobias >> >>> sessionInfo() >> R version 2.5.1 (2007-06-27) >> i386-apple-darwin8.9.1 >> >> locale: >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] "stats" "graphics" "grDevices" "utils" "datasets" >> "methods" "base" >> >> other attached packages: >> GEOquery >> "2.0.6" >> >> >> ====================================================================== >> Dr. Tobias Straub Adolf-Butenandt-Institute, Molecular Biology >> tel: +49-89-2180 75 439 Schillerstr. 44, 80336 Munich, Germany >> >> _______________________________________________ >> 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 > > ====================================================================== > Dr. Tobias Straub Adolf-Butenandt-Institute, Molecular Biology > tel: +49-89-2180 75 439 Schillerstr. 44, 80336 Munich, Germany > > _______________________________________________ > 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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org

Hi Tobias: I could not reproduce the error with R 2.5.0 and GEOquery 2.0.5 > library(GEOquery) > gse<-getGEO('GSE94') trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE94/GSE94_family .soft.gz' ftp data connection made, file length 100293949 bytes opened URL downloaded 97943Kb File stored at: C:\DOCUME~1\smohapat\LOCALS~1\Temp\RtmpabhBsb/GSE94.soft.gz Parsing.... ^PLATFORM = GPL218 ^SAMPLE = GSM2628 ^SAMPLE = GSM2629 ^SAMPLE = GSM2630 ^SAMPLE = GSM3514 ^SAMPLE = GSM3515 ^SAMPLE = GSM3516 ^SAMPLE = GSM3517 ^SAMPLE = GSM3518 ^SAMPLE = GSM3519 ^SAMPLE = GSM3520 ^SAMPLE = GSM3521 ^SAMPLE = GSM3522 ^SAMPLE = GSM3523 ^SAMPLE = GSM3524 ^SAMPLE = GSM3525 ^SAMPLE = GSM3526 ^SAMPLE = GSM3527 ^SAMPLE = GSM3528 ^SAMPLE = GSM3529 ^SAMPLE = GSM3530 ^SAMPLE = GSM3531 ^SAMPLE = GSM3532 ^SAMPLE = GSM3533 ^SAMPLE = GSM3534 ^SAMPLE = GSM3535 ^SAMPLE = GSM3536 ^SAMPLE = GSM3537 ^SAMPLE = GSM3538 ^SAMPLE = GSM3539 ^SAMPLE = GSM3540 ^SAMPLE = GSM3541 ^SAMPLE = GSM3542 ^SAMPLE = GSM3543 ^SAMPLE = GSM3544 ^SAMPLE = GSM3545 ^SAMPLE = GSM3546 ^SAMPLE = GSM3547 ^SAMPLE = GSM3548 ^SAMPLE = GSM3549 ^SAMPLE = GSM3550 ^SAMPLE = GSM3551 ^SAMPLE = GSM3552 ^SAMPLE = GSM3553 ^SAMPLE = GSM3554 ^SAMPLE = GSM3555 ^SAMPLE = GSM3556 ^SAMPLE = GSM3557 ^SAMPLE = GSM3558 ^SAMPLE = GSM3559 ^SAMPLE = GSM3560 ^SAMPLE = GSM3561 ^SAMPLE = GSM3562 ^SAMPLE = GSM3563 ^SAMPLE = GSM3564 ^SAMPLE = GSM3565 ^SAMPLE = GSM3566 ^SAMPLE = GSM3567 ^SAMPLE = GSM3568 ^SAMPLE = GSM3569 ^SAMPLE = GSM3570 ^SAMPLE = GSM3571 ^SAMPLE = GSM3572 ^SAMPLE = GSM3573 ^SAMPLE = GSM3574 ^SAMPLE = GSM3575 ^SAMPLE = GSM3576 ^SAMPLE = GSM3577 ^SAMPLE = GSM3578 ^SAMPLE = GSM3579 ^SAMPLE = GSM3580 ^SAMPLE = GSM3581 ^SAMPLE = GSM3582 ^SAMPLE = GSM3583 ^SAMPLE = GSM3584 ^SAMPLE = GSM3585 ^SAMPLE = GSM3586 ^SAMPLE = GSM3587 ^SAMPLE = GSM3588 ^SAMPLE = GSM3589 ^SAMPLE = GSM3590 ^SAMPLE = GSM3591 ^SAMPLE = GSM3592 ^SAMPLE = GSM3593 ^SAMPLE = GSM3594 ^SAMPLE = GSM3595 ^SAMPLE = GSM3596 ^SAMPLE = GSM3597 ^SAMPLE = GSM3598 ^SAMPLE = GSM3599 ^SAMPLE = GSM3600 ^SAMPLE = GSM3601 ^SAMPLE = GSM3602 ^SAMPLE = GSM3603 ^SAMPLE = GSM3604 ^SAMPLE = GSM3605 ^SAMPLE = GSM3606 ^SAMPLE = GSM3607 ^SAMPLE = GSM3608 ^SAMPLE = GSM3609 ^SAMPLE = GSM3610 ^SAMPLE = GSM3611 ^SAMPLE = GSM3612 ^SAMPLE = GSM3613 ^SAMPLE = GSM3614 ^SAMPLE = GSM3615 ^SAMPLE = GSM3616 ^SAMPLE = GSM3617 ^SAMPLE = GSM3618 ^SAMPLE = GSM3619 ^SAMPLE = GSM3620 ^SAMPLE = GSM3621 ^SAMPLE = GSM3622 ^SAMPLE = GSM3623 ^SAMPLE = GSM3624 ^SAMPLE = GSM3625 ^SAMPLE = GSM3626 ^SAMPLE = GSM3627 ^SAMPLE = GSM3628 ^SAMPLE = GSM3629 ^SAMPLE = GSM3630 ^SAMPLE = GSM3631 ^SAMPLE = GSM3632 ^SAMPLE = GSM3633 ^SAMPLE = GSM3634 ^SAMPLE = GSM3635 ^SAMPLE = GSM3636 ^SAMPLE = GSM3637 ^SAMPLE = GSM3638 ^SAMPLE = GSM3639 ^SAMPLE = GSM3640 ^SAMPLE = GSM3641 ^SAMPLE = GSM3642 ^SAMPLE = GSM3643 ^SAMPLE = GSM3644 ^SAMPLE = GSM3645 ^SAMPLE = GSM3646 ^SAMPLE = GSM3647 ^SAMPLE = GSM3648 ^SAMPLE = GSM3649 ^SAMPLE = GSM3650 ^SAMPLE = GSM3651 ^SAMPLE = GSM3652 ^SAMPLE = GSM3653 ^SAMPLE = GSM3654 ^SAMPLE = GSM3655 ^SAMPLE = GSM3656 ^SAMPLE = GSM3657 ^SAMPLE = GSM3658 ^SAMPLE = GSM3659 ^SAMPLE = GSM3660 ^SAMPLE = GSM3661 ^SAMPLE = GSM3662 ^SAMPLE = GSM3663 ^SAMPLE = GSM3664 ^SAMPLE = GSM3665 ^SAMPLE = GSM3666 ^SAMPLE = GSM3667 ^SAMPLE = GSM3668 > sessionInfo() R version 2.5.0 (2007-04-23) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" other attached packages: GEOquery "2.0.5" > Best, Saroj Tobias Straub wrote: >I tried to fetch and parse the GSE94 series from GEO using GEOquery >library (gse<-getGEO('GSE94')). Operation is aborted with the message: > >Error in make.names(as.character(names), allow_) : > invalid multibyte string 29 >In addition: There were 12 warnings (use warnings() to see them) > >is that an error of getGEO or a problem of the data set? > >Tobias > > > sessionInfo() >R version 2.5.1 (2007-06-27) >i386-apple-darwin8.9.1 > >locale: >en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >attached base packages: >[1] "stats" "graphics" "grDevices" "utils" "datasets" >"methods" "base" > >other attached packages: >GEOquery >"2.0.6" > > >===================================================================== = >Dr. Tobias Straub Adolf-Butenandt-Institute, Molecular Biology >tel: +49-89-2180 75 439 Schillerstr. 44, 80336 Munich, Germany > >_______________________________________________ >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 > >

ok, I figured it out myself! modified GEOquery *** GEOquery Fri Aug 10 08:24:53 2007 --- GEOquery_new Fri Aug 31 14:43:15 2007 *************** *** 495,500 **** --- 495,501 ---- nextEntity <- "" while(!finished) { line <- readLines(con,1) + line <- iconv(line, "LATIN2", "UTF-8") if(length(line)==0) finished <- TRUE a[lines] <- line lines <- lines+1 *************** *** 510,515 **** --- 511,517 ---- finished <- FALSE while(!finished) { line <- readLines(con,1) + line <- iconv(line, "LATIN2", "UTF-8") if(length(line)==0) { finished <- TRUE } else { On Aug 31, 2007, at 2:17 PM, Tobias Straub wrote: > I tried to fetch and parse the GSE94 series from GEO using GEOquery > library (gse<-getGEO('GSE94')). Operation is aborted with the message: > > Error in make.names(as.character(names), allow_) : > invalid multibyte string 29 > In addition: There were 12 warnings (use warnings() to see them) > > is that an error of getGEO or a problem of the data set? > > Tobias > >> sessionInfo() > R version 2.5.1 (2007-06-27) > i386-apple-darwin8.9.1 > > locale: > en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] "stats" "graphics" "grDevices" "utils" "datasets" > "methods" "base" > > other attached packages: > GEOquery > "2.0.6" > > > ====================================================================== > Dr. Tobias Straub Adolf-Butenandt-Institute, Molecular Biology > tel: +49-89-2180 75 439 Schillerstr. 44, 80336 Munich, Germany > > _______________________________________________ > 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 ====================================================================== Dr. Tobias Straub Adolf-Butenandt-Institute, Molecular Biology tel: +49-89-2180 75 439 Schillerstr. 44, 80336 Munich, Germany