[BioC] error massage = subscript out of bounds

[Wolfgang Huber]

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 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 at kispi.uzh.ch <mailto:Regina.Hecker at kispi.uzh.ch> 
> 
> 
> 
> 
> 
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