[BioC] Affymetrix US Rice Gene Strip 1.1

[cstrato]

Dear Nick,

Jim has already told you how to build the annotation package for use 
with oligo.

For xps you need the same library and annotation files from Affymetrix 
that Jim has listed. Then you could do the following to create the 
'scheme' file for the RUSGene array:

library(xps)

# directory containing Affymetrix library files
libdir <- "/Volumes/GigaDrive/Affy/libraryfiles"

# directory containing Affymetrix annotation files
anndir <- "/Volumes/GigaDrive/Affy/Annotation"

# directory to store ROOT scheme files
scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"

# create scheme file for RUSGene-1_1-st-v1:
scheme.rusgene11stv1 <- import.exon.scheme("rusgene11stv1", filedir = 
file.path(scmdir, "designtime"),
                         file.path(libdir, "RUSGene-1_1-st_rev2", 
"RUSGene-1_1-st.clf"),
                         file.path(libdir, "RUSGene-1_1-st_rev2", 
"RUSGene-1_1-st.pgf"),
                         file.path(anndir, "ModelOrganisms", 
"RUSGene-1_1-st-v1.design-time.20130417.probeset.csv"),
                         file.path(anndir, "ModelOrganisms", 
"RUSGene-1_1-st-v1.design-time.20130417.transcript.csv"))


However, since the annotation files are design-time files they are 
missing some header information which is usually included and checked by 
xps. Thus currently you need to add two lines to each header file.

For RUSGene-1_1-st-v1.design-time.20130417.probeset.csv you need to add 
the following two lines to the header (order is not important):
#%netaffx-annotation-netaffx-build=NA
#%netaffx-annotation-data-type=probe_set

For RUSGene-1_1-st-v1.design-time.20130417.transcript.csv you need to 
add the following two lines to the header (order is not important):
#%netaffx-annotation-netaffx-build=NA
#%netaffx-annotation-data-type=transcript_cluster

During the weekend I will upload an updated version 'xps_1.20.2' to 
Bioconductor so that correction of the design-time annotation files is 
no longer necessary.

Best regards,
Christian


On 5/9/13 12:00 AM, James W. MacDonald 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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>