Dear Bioconductor-Team, I am currently using the R-package cellHTS to analyse RNAi screening data. As I have not worked with R before, I modify the vignette "analysis of multi-channel cell-based screens" according to my experiment. After defining my controls I perform the writeReport command and get the follwing error: > out <- writeReport(cellHTSlist = list(raw = x), outdir = "raw- pgl4-",posControls = posControls, negControls = negControls) cellHTS2 is busy creating HTML pages for 'AP2betapGl4'. Found raw data. State: configured=TRUE, annotated=FALSE 0% done (step 1 of 6) 17% done (step 2 of 6) 24% done (step 3 of 6)Fehler in b[i:(da[1] + i - 1), j:(da[2] + j - 1)] = a : Indizierung außerhalb der Grenzen Zusätzlich: Warning message: The 'cellHTSlist' argument is deprecated. Please provide all necessary cellHTS objects separately via the 'raw', 'normalized' and 'scored' arguments` As I cannot identify the source of the error, I am not sure what it means or which files / commands I will have to change. Do you have any experience with this or could you explain this error to a novel Biocondutor user? Thanks a lot, Regina _____________________________ Regina Hecker Ph.D. Student University Children's Hospital Zürich Division of Oncology August Forel Str.1 8008 Zürich Tel. +41 44 634 8801 Fax. +41 44 634 8859 e-mail: Regina.Hecker@kispi.uzh.ch <mailto:regina.hecker@kispi.uzh.ch> ********************************************************************** ************************ IMPORTANT: The contents of this email and any attachments are confidential. They are intended for the named recipient(s) only. If you have received this email in error, please notify the system manager or the sender immediately and do not disclose the contents to anyone or make copies thereof. *** eSafe scanned this email for viruses, vandals, and malicious content. *** ********************************************************************** ************************ [[alternative HTML version deleted]]

Dear Regina in order to help us helping you with this, can you provide the output of sessionInfo(), as well as with the means to reproduce your problem, i.e to obtain from you (or recreate) the objects "x", "posControls", "negControls" used in your code? Also, your post is not clear whether you use "cellHTS" or "cellHTS2". While their use cases are similar, the user interface and functionality of cellHTS2 has improved a lot, and this is what I now recommend using. For using cellHTS2, please refer to the documentation of cellHTS2 (and not of cellHTS). Best wishes Wolfgang ------------------------------------------------ Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber > Dear Bioconductor-Team, > > I am currently using the R-package cellHTS to analyse RNAi screening data. As I have not worked with R before, I modify the vignette "analysis of multi-channel cell-based screens" according to my experiment. After defining my controls I perform the writeReport command and get the follwing error: > > > >> out <- writeReport(cellHTSlist = list(raw = x), outdir = "raw- pgl4-",posControls = posControls, negControls = negControls) > > cellHTS2 is busy creating HTML pages for 'AP2betapGl4'. > > Found raw data. > > State: > > configured=TRUE, annotated=FALSE > > 0% done (step 1 of 6) > > 17% done (step 2 of 6) > > 24% done (step 3 of 6)Fehler in b[i:(da[1] + i - 1), j:(da[2] + j - 1)] = a : > > Indizierung au?erhalb der Grenzen > > Zus?tzlich: Warning message: > > The 'cellHTSlist' argument is deprecated. > > Please provide all necessary cellHTS objects separately via the 'raw', 'normalized' and 'scored' arguments` > > > > > > As I cannot identify the source of the error, I am not sure what it means or which files / commands I will have to change. > > Do you have any experience with this or could you explain this error to a novel Biocondutor user? > > Thanks a lot, > > Regina > > _____________________________ > > > > Regina Hecker > > Ph.D. Student > > University Children's Hospital Z?rich > Division of Oncology > August Forel Str.1 > 8008 Z?rich > > > > Tel. +41 44 634 8801 > Fax. +41 44 634 8859 > > > > e-mail: Regina.Hecker at kispi.uzh.ch <mailto:regina.hecker at="" kispi.uzh.ch=""> > > > > > > ******************************************************************** ************************** > IMPORTANT: The contents of this email and any attachments are confidential. They are intended for the > named recipient(s) only. > If you have received this email in error, please notify the system manager or the sender immediately and do > not disclose the contents to anyone or make copies thereof. > *** eSafe scanned this email for viruses, vandals, and malicious content. *** > ******************************************************************** ************************** > [[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 --

The problem was caused by a bug in the cellHTS2 package which has been fixed in the latest devel version (2.9.6). The fix has also been pushed back into the release branch (version 2.8.1) Florian On 05.06.2009, at 16:42, Hecker Regina wrote: > Dear Bioconductor-Team, > > I am currently using the R-package cellHTS to analyse RNAi screening > data. As I have not worked with R before, I modify the vignette > "analysis of multi-channel cell-based screens" according to my > experiment. After defining my controls I perform the writeReport > command and get the follwing error: > > > >> out <- writeReport(cellHTSlist = list(raw = x), outdir = "raw- >> pgl4-",posControls = posControls, negControls = negControls) > > cellHTS2 is busy creating HTML pages for 'AP2betapGl4'. > > Found raw data. > > State: > > configured=TRUE, annotated=FALSE > > 0% done (step 1 of 6) > > 17% done (step 2 of 6) > > 24% done (step 3 of 6)Fehler in b[i:(da[1] + i - 1), j:(da[2] + j - > 1)] = a : > > Indizierung au?erhalb der Grenzen > > Zus?tzlich: Warning message: > > The 'cellHTSlist' argument is deprecated. > > Please provide all necessary cellHTS objects separately via the > 'raw', 'normalized' and 'scored' arguments` > > > > > > As I cannot identify the source of the error, I am not sure what it > means or which files / commands I will have to change. > > Do you have any experience with this or could you explain this error > to a novel Biocondutor user? > > Thanks a lot, > > Regina > > _____________________________ > > > > Regina Hecker > > Ph.D. Student > > University Children's Hospital Z?rich > Division of Oncology > August Forel Str.1 > 8008 Z?rich > > > > Tel. +41 44 634 8801 > Fax. +41 44 634 8859 > > > > e-mail: Regina.Hecker at kispi.uzh.ch <mailto:regina.hecker at="" kispi.uzh.ch=""> > > > > > > ******************************************************************** ************************** > IMPORTANT: The contents of this email and any attachments are > confidential. They are intended for the > named recipient(s) only. > If you have received this email in error, please notify the system > manager or the sender immediately and do > not disclose the contents to anyone or make copies thereof. > *** eSafe scanned this email for viruses, vandals, and malicious > content. *** > ******************************************************************** ************************** > [[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