[BioC] Dilution

[Robert Gentleman]

Yuan Jian wrote:
> Hi Robert,
> thanks for your reply. I tried several time to reinstall packages, but 
> failed to find solution.

  I don't see why that is a reason to ignore the posting guide.

   Did you use biocLite to install? The instructions are pretty clear, 
and if you follow them you are less likely to have these sorts of problems.

   As Kasper pointed out, you have an old affydata (at least), and using
  biocLite would have prevented that from happening (and if not please 
give us details).

> here is seeeionInfor:
>  > sessionInfo()
> R version 2.6.1 (2007-11-26)
> i386-pc-mingw32
> locale:
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
> attached base packages:
> [1] tools     stats     graphics  grDevices datasets  utils     
> methods   base    
> other attached packages:
>  [1] hgu95av2cdf_2.0.0      affydata_1.4.0         
> preprocessCore_1.0.0   affyio_1.6.1           Biobase_1.16.2       
>  [6] aroma.affymetrix_0.8.3 affy_1.16.0            
> aroma.apd_0.1.3        R.huge_0.1.5           digest_0.3.1         
> [11] aroma.light_1.6.0      affxparser_1.10.2      
> R.rsp_0.3.3            R.cache_0.1.6          EBImage_2.2.0        
> [16] R.utils_0.9.8          R.oo_1.4.1             R.methodsS3_1.0.0    
> 
> 
> */Robert Gentleman <rgentlem at fhcrc.org>/* wrote:
> 
>     Hi Yuan,
>     Please read the posting guide for this mailing list and follow the
>     directions there, and especially provide the output of sessionInfo.
> 
>     I don't see any problems with these commands, so I suspect you have
>     some issues with your installation.
> 
>     best wishes
>     Robert
> 
>     Yuan Jian wrote:
>      > Hello,
>      >
>      > I have struggled the following simple commands for long time, can
>     you please fix the problem?
>      >
>      > > library("affydata")
>      >> data(Dilution)
>      >> pm(Dilution, "1001_at")[1:3, ]
>      > Error in assayData(object) :
>      > no slot of name "assayData" for this object of class "AffyBatch"
>      >
>      > Thanks
>      > Yuan
>      >
>      >
>      >
>      > ---------------------------------
>      >
>      > [[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
>      >
> 
>     -- 
>     Robert Gentleman, PhD
>     Program in Computational Biology
>     Division of Public Health Sciences
>     Fred Hutchinson Cancer Research Center
>     1100 Fairview Ave. N, M2-B876
>     PO Box 19024
>     Seattle, Washington 98109-1024
>     206-667-7700
>     rgentlem at fhcrc.org
> 
> 
> ------------------------------------------------------------------------
> Looking for last minute shopping deals? Find them fast with Yahoo! 
> Search. 
> <http://us.rd.yahoo.com/evt=51734/*http://tools.search.yahoo.com/newsearch/category.php?category=shopping> 
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org