[BioC] Dilution

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Thu Jan 24 07:53:37 CET 2008


On Jan 23, 2008, at 10:44 PM, Yuan Jian wrote:

> Hi Kasper,
>   thank you very much. it worked.
>   another similar problem is

If the problem is similar, why don't you try the same solution? Do  
what Benilton asks you to.

Kasper


>> 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 at 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 at fhcrc.org
>>
>>
>>
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>
>
>
>
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