Hi Kasper,
  thank you very much. it worked.
  another similar problem is
   
  > library("ALLMLL")
> data(MLL.B)
Warning message:
'MLL.B' looks like a pre-2.4.0 S4 object: please recreate it 
> Data <-MLL.B[,c(2,1,3:5,14,6,13)]
Error in MLL.B[, c(2, 1, 3:5, 14, 6, 13)] : 
  incorrect number of dimensions

  this command is from "Bioinformatics and Computational Biology Solutions using R and
  Bioconductor" edited by R Gentleman, et. al 
   
  can you please tell me how to "recreate MLL.B"?
   
  > 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] ALLMLL_1.0             hgu95av2cdf_2.0.0      affydata_1.4.0         preprocessCore_1.0.0   affyio_1.6.1          
 [6] Biobase_1.16.2         aroma.affymetrix_0.8.3 affy_1.16.0            aroma.apd_0.1.3        R.huge_0.1.5          
[11] digest_0.3.1           aroma.light_1.6.0      affxparser_1.10.2      R.rsp_0.3.3            R.cache_0.1.6         
[16] EBImage_2.2.0          R.utils_0.9.8          R.oo_1.4.1             R.methodsS3_1.0.0     
> 

  

Kasper Daniel Hansen <khansen@stat.Berkeley.EDU> wrote:
  You might want to do an
Dilution = updateObject(Dilution)
my guess is that you are using a recent version of affy/Biobase with 
an old version of the Dilution dataset. You could also just re- 
install Dilution, that should fix it (assuming that you are running a 
recent version of R etc)

Kasper

On Jan 23, 2008, at 9:43 PM, Yuan Jian wrote:

> Hi Robert,
> thanks for your reply. I tried several time to reinstall 
> packages, but failed to find solution.
> 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 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
>>
>>
>>
>> ---------------------------------
>>
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>>
>
> -- 
> 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@fhcrc.org
>
>
>
> ---------------------------------
>
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