[BioC] error message

[Robert Gentleman]

Then please supply the output of sessionInfo() and at least some of the 
input you used.  How did you install the packages, please supply the 
commands you used, don't say: "I followed the instructions", that is too 
vague and presumes that you made no errors doing that.  There are very 
many things that could go wrong, and you will need to provide a great 
deal more information before anyone could help you.


Chintanu wrote:
> Dear Wolfgang,
> 
> Thanks for your reply !
> 
> Regarding the error-message, I have it even reinstalled (following the
> instructions from Bioconductor webpage), but still getting no escape from
> it. While searching on the web on it, I didn't get the solution but found
> people mentioning about it:
> 
> http://www.google.com/search?hl=en&q=%22is+not+a+valid+package+--+installed+%3C+2.0.0%3F%22&btnG=Search
> 
> Cheers,
> Chintanu
> 
> = = = = = =  = = = = =  = = = = = = =
> 
> 
> On Feb 9, 2008 1:00 AM, Wolfgang Huber <huber at ebi.ac.uk> wrote:
> 
>> Dear Chintanu,
>>
>> the target file can be (needs to be) produced by you, it is a way of
>> telling the various subsequent analysis methods which biological samples
>> were on which array, which colour etc.
>>
>> Regarding installation, please do follow the instructions at
>> http://www.bioconductor.org/download
>>
>> Best wishes
>>  Wolfgang
>>
>> ------------------------------------------------------------------
>> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>>
>>
>> Chintanu scripsit:
>>> Hi All,
>>>
>>> I'm a novice both to R and microarray, and am struggling to learn both
>> by
>>> myself.  Currently, I have got a microarray dataset from a research lab
>>> which contains cDNA and Affymetrix data files. The R-based literature
>> refers
>>> many times to a file that contains target description (a .txt file with
>>> names like target.txt). But my dataset interestingly doesn't have any of
>>> such files. I am now struggling to find out how important this .txt file
>> is
>>> as otherwise I have all the relevant image processing output files (e.g
>> .,
>>> .gpr file). From the literature, I do understand that the so-called
>> 'target
>>> file' contains information about the RNA samples used as targets in the
>>> microarray experiment, yet I'm wondering whether such files may be
>> created
>>> at one's end too. Or, is it ONLY the relevant lab which can give me this
>>> file and else I can't move ahead!
>>>
>>>
>>>
>>> However, I do see that there is an information file in the dataset which
>>> talks about the patient's name, file name and so on, but somehow I am
>>> pessimistic that this is the file I am looking for (a part of it is
>> attached
>>> below).
>>>
>>>
>>>
>>> Patients   File         Cy5                Cy3
>>> Gal_File
>>>                    GenePix            Notes
>>>
>>> PreB1     B1a         Test               Control Pool
>>> HS_10.5K_GP.gal
>>> Pro 3.0
>>>
>>>               B1b         Test               Control Pool
>>> HS_10.5K_GP.gal                 Pro 3.0
>>>
>>>               B1cDS    Control Pool     Test
>>> HS_10.5K_GP.gal                 Pro 3.0             Dye Swap
>>>
>>> PreB2    B2a         Test                Control Pool
>>> HS_10.5K_GP.gal
>>> Pro 3.0
>>>
>>>              B2b         Test                Control Pool
>>> PMCI_10.5KSC_GP.gal         Pro 3.0
>>>
>>>              B2cDS    Control Pool     Test
>>> HS_10.5K_GP.gal                 Pro 3.0             Dye Swap
>>>
>>>
>>>
>>>
>>> *Part 2*:
>>>
>>> I'm also struggling to figure out why I get error messages, as below,
>> while
>>> loading certain packages and whether there is a way to correct this
>> problem
>>> .
>>>
>>>
>>> library(marrayPlots)
>>> Error in library(marrayPlots) :
>>> 'marrayPlots' is not a valid package -- installed < 2.0.0?
>>>
>>>
>>>
>>> library(marrayNorm)
>>> Error in library(marrayNorm) :
>>> 'marrayNorm' is not a valid package -- installed < 2.0.0?
>>>
>>>
>>> May I request you to kindly reply and help me out, please !
>>>
>>> Cheers,
>>>
>>> Chintanu
>>>
>>>       [[alternative HTML version deleted]]
> 
> 	[[alternative HTML version deleted]]
> 
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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