[BioC] Affymetrix US Rice Gene Strip 1.1

[James W. MacDonald]

On 5/9/2013 11:37 AM, Nicholas Lawson wrote:
> I'm so sorry Jim, I found my typo in AffyGenePDInfoPkgSeed! I was missing the Pkg, but now I am getting:
>
> error in validObject(.Object) :
> invalid class “ScalarCharacter” object: ScalarCharacter must have length one

Almost surely this is because of the email address issue that I 
mentioned in my previous email.

Best,

Jim


>
> Thanks,
> Nick
>
> On May 9, 2013, at 10:32 AM, Nicholas Lawson<nll001 at email.uark.edu>  wrote:
>
>> Sorry here is the whole error message:
>>
>> Error in getClass(Class, where = topenv(parent.frame())) :
>>   “AffyGenePDInfoSeed” is not a defined class
>>
>>
>> -Nick
>>
>>
>> On May 9, 2013, at 10:27 AM, Nicholas Lawson<nll001 at email.uark.edu>  wrote:
>>
>>> Thank you so much for the help. However, I have ran into another problem and I have tried googling with no success. Now I am running into a new error
>>>
>>> error: “AffyGenePDInfoSeed” is not a defined class
>>>
>>> This is when I'm trying to create seed using:
>>> 	seed<- new("AffyGenePDInfoSeed", pdfFile = pgf, clfFile = clf, transFile = trans, prodeFile = prob, author = 			"Nick Lawson", email = "nll001 at email.uark.edu", biocViews = "AnnotationData", organism = "Rice", species = 		"Oryza saliva")
>>>
>>> Thanks Again,
>>> Nick
>>>
>>> On May 8, 2013, at 5:00 PM, James W. MacDonald<jmacdon at uw.edu>  wrote:
>>>
>>>> Hi Nick,
>>>>
>>>> You can't use the affy package for this analysis. Instead you need to use either oligo or xps. I can't help with xps, but perhaps Christian Stratowa will give you some hints.
>>>>
>>>> For oligo you will need to build some packages. First, get the files here:
>>>>
>>>> http://www.affymetrix.com/Auth/analysis/downloads/lf/wt/RUSGene-1_1-st-v1/RUSGene-1_1-st_rev2.zip
>>>> http://www.affymetrix.com/Auth/analysis/downloads/lf/wt/RUSGene-1_1-st-v1/RUSGene-1_1-st-v1.design-time.20130417.zip
>>>>
>>>> and unzip somewhere. You then need to build a pd.info package. So install pdInfoBuilder using biocLite(), and then follow the instructions here:
>>>>
>>>> https://stat.ethz.ch/pipermail/bioconductor/2013-March/051335.html
>>>>
>>>> You essentially want to be able to tell pdInfoBuilder where these files are:
>>>>
>>>> RUSGene-1_1-st.mps
>>>> RUSGene-1_1-st.pgf
>>>> RUSGene-1_1-st.clf
>>>> RUSGene-1_1-st-v1.design-time.20130417.probeset.csv
>>>> RUSGene-1_1-st-v1.design-time.20130417.transcript.csv
>>>>
>>>> You can just pull them out of the unzipped files and put them somewhere convenient, and then follow what Kamila did in the above referenced BioC mail message. Once you have built the package you will have to install it. Usually something like
>>>>
>>>> install.packages("<filename goes here>", repos=NULL, type="source")
>>>>
>>>> will do the trick.
>>>>
>>>> Best,
>>>>
>>>> Jim
>>>>
>>>>
>>>>
>>>>
>>>> On 5/8/2013 5:28 PM, Nicholas Lawson [guest] wrote:
>>>>> Hello,
>>>>> 	I am trying to use bioconductor to run analysis on my Affymetrix Gene Strip array data. I have loaded just about everything I can find to load, libraries and packages. However, I keep getting an error in getCdfInfo(object): Specified environment does not contain RUSGene-1_1-st Library - package rusgene11stcdf not installed. Then I try to run biocLite(rusgene11stcdf) and it tells me that 'rusgene11stcdf' is not available. I tried downloading a folder from affymetrix that has info on the RUS gene st array but there are no cdc files in that. Please help!
>>>>>
>>>>> Thanks,
>>>>> Nick Lawson
>>>>>
>>>>> -- output of sessionInfo():
>>>>>
>>>>>> eset<- justRMA()
>>>>> Error in getCdfInfo(object) :
>>>>> Could not obtain CDF environment, problems encountered:
>>>>> Specified environment does not contain RUSGene-1_1-st
>>>>> Library - package rusgene11stcdf not installed
>>>>> Bioconductor - rusgene11stcdf not available
>>>>>
>>>>> --
>>>>> Sent via the guest posting facility at bioconductor.org.
>>>>>
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>>>> -- 
>>>> James W. MacDonald, M.S.
>>>> Biostatistician
>>>> University of Washington
>>>> Environmental and Occupational Health Sciences
>>>> 4225 Roosevelt Way NE, # 100
>>>> Seattle WA 98105-6099
>>>>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099