[BioC] Dilution
Martin Morgan
mtmorgan at fhcrc.org
Thu Jan 24 15:08:35 CET 2008
Hi Yuan --
A general procedure for updating packages is on the Bioconductor web
site http://bioconductor.org/download, under 'Update packages': in a
new R session (e.g., R --vanilla)
> source('http://bioconductor.org/biocLite.R')
> update.packages(repos=biocinstallRepos())
(add the argument ask=FALSE if you have many packages requiring
update and trust that all will be updated correctly).
As people are trying to be helpful and provide advice to you, I'll add
a suggestion that an effective strategy for 'debugging' is to make
things as simple as possible. So by the time I'm posting a question to
this list my sessionInfo() will contain only the packages required to
reproduce the problem (no need for 19 packages to demonstrate an
out-of-date MLL.B!), and the example will be stripped to its barest
minimum, e.g., your subsetting statement might be reduced to Data <-
MLL.B[,1]. You (or others reading this post and following its advice)
might discover in the process that the 'bug' is actually a simple
typo, or not related to what it appeared to be, or otherwise resolve
the issue. You'll also make it easier for those with experience to
spot the problem, and hence offer a solution.
Another resource is the Bioconductor mailing list archives and the
search facilities (not altogether satisfactory, I admit), again linked
from the Bioconductor home page. The problem of old Dilution data sets
was common a year or so ago when most people transitioned from R 2.4
to 2.5 (I think; it might have been 2.3 to 2.4).
Martin
Yuan Jian <jayuan2008 at yahoo.com> writes:
> 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 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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>> gmane.science.biology.informatics.conductor
>
>
>
>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
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