Lumi and Beadstudio 1.5.13
1
0
Entering edit mode
@claudioisliberoit-1075
Last seen 9.6 years ago
dear all, I recently tried to reload some old data anlysis which encompasses Illumina data from beastudio 1.5.13. Notably a chunck of code that previously work now does not any more. in particular: > filenames <- "myData.txt" > > r <- lumiR(filenames) Error in `[.data.frame`(annotation, , "PROBE_SEQUENCE") : undefined columns selected looking in the man it seems that the package was updated to the new Illumina Bead Studio output. looking in the ma I guessed to put inputAnnotation=FALSE. but still nothing. r <- lumiR(filenames, inputAnnotation=FALSE) Error in `[.data.frame`(annotation, , "PROBE_SEQUENCE") : undefined columns selected Now, I dont have the new software. what can I do? > sessionInfo() R version 2.7.2 (2008-08-25) 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] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] lumi_1.6.2 mgcv_1.4-1 affy_1.18.2 [4] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1
• 800 views
ADD COMMENT
0
Entering edit mode
Pan Du ★ 1.2k
@pan-du-2010
Last seen 9.6 years ago
Hi Claudio, Thanks for reporting the problem. I am not sure why it reported error when retrieving a missing column in a data.frame, usually it should return NULL instead of reporting error. To avoid this, please set the parameter convertNuID as FALSE, e.g., r <- lumiR(filenames, convertNuID=FALSE) It should solve the problem. Tell me if the problem still exists. Pan On 9/5/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch" <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > Date: Thu, 4 Sep 2008 12:04:29 +0200 > From: "claudio\.is\@libero\.it" <claudio.is at="" libero.it=""> > Subject: [BioC] Lumi and Beadstudio 1.5.13 > To: "bioconductor" <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <k6o1bh$de2008fc6621fdeff2634e135b59a423 at="" libero.it=""> > Content-Type: text/plain; charset=iso-8859-1 > > dear all, > > I recently tried to reload some old data anlysis which encompasses Illumina > data from beastudio 1.5.13. > > Notably a chunck of code that previously work now does not any more. > in particular: > >> filenames <- "myData.txt" >> >> r <- lumiR(filenames) > Error in `[.data.frame`(annotation, , "PROBE_SEQUENCE") : > undefined columns selected > > > looking in the man it seems that the package was updated to the new Illumina > Bead Studio output. > > looking in the ma I guessed to put inputAnnotation=FALSE. but still nothing. > > r <- lumiR(filenames, inputAnnotation=FALSE) > Error in `[.data.frame`(annotation, , "PROBE_SEQUENCE") : > undefined columns selected > > Now, I dont have the new software. what can I do? > > >> sessionInfo() > R version 2.7.2 (2008-08-25) > 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;L > C_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] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] lumi_1.6.2 mgcv_1.4-1 affy_1.18.2 > [4] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 ------------------------------------------------------ Pan Du, PhD Research Assistant Professor Northwestern University Biomedical Informatics Center 750 N. Lake Shore Drive, 11-176 Chicago, IL 60611 Office (312) 503-2360; Fax: (312) 503-5388 dupan at northwestern.edu
ADD COMMENT

Login before adding your answer.

Traffic: 860 users visited in the last hour
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