I have a R program reading data file of Illmina Human Whole Genome Bead Array. BSData = readBeadSummaryData(dataFile = dataFile, ProbeID="PROBE_ID", skip=0) This line works fine in R 2.11.1, but not in R 2.12.0. It gives me something like Error in readBeadSummaryData(dataFile = dataFile, ProbeID = "PROBE_ID", : object 'QC' not found A bug in new beadarray package maybe? Any Comment? > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Chinese_Taiwan.950 LC_CTYPE=Chinese_Taiwan.950 LC_MONETARY=Chinese_Taiwan.950 [4] LC_NUMERIC=C LC_TIME=Chinese_Taiwan.950 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] beadarray_2.0.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] limma_3.6.0 Weihsin Wang, Ph.D. Bioinformatics Core Lab., Biomedical Engineering Research Lab., Industrial Technology Research Institute TEL:886-3-5913689 FAX: 886-3-5820445 ==================================================================== æœ¬ä¿¡ä»¶å¯èƒ½åŒ å«å·¥ç ”é™¢æ©Ÿå¯†è³‡è¨Šï¼ŒéžæŒ‡å®šä¹‹æ”¶ä»¶è€ ï¼Œè«‹å‹¿ä½¿ç”¨æˆ–æ­éœ²æœ¬ä¿¡ä»¶å §å®¹ï¼Œä¸¦è«‹éŠ·æ¯€æ­¤ä¿¡ä»¶ã€‚ This email may contain confidential information. Please do not use or disclose it in any way and delete it if you are not the intended recipient. [[alternative HTML version deleted]]

Hi, Yes, unfortunately this is a bug introduced in the new version of beadarray. The error is triggered when no qcFile is specified in readBeadSummaryData. If you have a qcFile then the code should run Ok. The bug is easy to fix and I will commit the fix in the latest version within the next day or so. Best wishes, Mark On Wed, Oct 20, 2010 at 7:59 AM, <jrwang at="" itri.org.tw=""> wrote: > I have a R program reading data file of Illmina Human Whole Genome Bead Array. > > BSData = readBeadSummaryData(dataFile = dataFile, ProbeID="PROBE_ID", skip=0) > > This line works fine in R 2.11.1, but not in R 2.12.0. It gives me something like > > Error in readBeadSummaryData(dataFile = dataFile, ProbeID = "PROBE_ID", : > object 'QC' not found > A bug in new beadarray package maybe? Any Comment? > >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i386-pc-mingw32/i386 (32-bit) > locale: > [1] LC_COLLATE=Chinese_Taiwan.950 LC_CTYPE=Chinese_Taiwan.950 LC_MONETARY=Chinese_Taiwan.950 > [4] LC_NUMERIC=C LC_TIME=Chinese_Taiwan.950 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] beadarray_2.0.0 Biobase_2.10.0 > loaded via a namespace (and not attached): > [1] limma_3.6.0 > Weihsin Wang, Ph.D. > Bioinformatics Core Lab., > Biomedical Engineering Research Lab., > Industrial Technology Research Institute > TEL:886-3-5913689 > FAX: 886-3-5820445 > > > ==================================================================== > ???????????????????????????????????????????? > This email may contain confidential information. Please do not use or disclose it in any way and delete it if you are not the intended recipient. > [[alternative HTML version deleted]] > > > _______________________________________________ > 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 >