[BioC] use of huex10stv2cdf_1.15.0.tar.gz and human exon array analysis

[Dan Strumpf]

Dear Christian,

Thanks for clarifying those points about xps. I'll look up the example 
scripts and will follow-up with you as needed.

Cheers,

Dan

cstrato wrote:
> Dear Dan
> 
> As the author of xps please allow me to answer your follow-up questions 
> regarding xps:
> 
> Michal has already mentioned that xps uses the PGF, CLF and annotation 
> files provided by Affymetrix. However, internally these files are 
> converted to a standard format for xps, so that you need to import these 
> files only once, see the help file ?import.exon.scheme.
> 
> Regarding the  documentation:
> Although the vignette deals only with the basics, it mentions two files 
> located in subdirectory xps/examples, namely "script4xps.R" and 
> "script4exon.R". Both scripts contain code examples which you mostly 
> need to only copy/paste.
> 
> File "script4exon.R" uses the Affymetrix human tissue-mixture exon array 
> dataset as an example how to process the HuExon array data as well as 
> the HGU133Plus2 data and the HuGene data.
> 
> Maybe one note on detection of differential analysis:
> Although "limma" is surely the preferred package, xps has also functions 
> for filtering of data before further analysis, and for detecting 
> differentially expressed genes, when there are only two groups ( see 
> Chapter 5 of vignette xps.pdf)
> 
> Please let me know if you have further questions.
> 
> Best regards
> Christian
> 
> 
> Dan Strumpf wrote:
>> Hi Michal,
>>
>> Thanks for your reply and suggestions! Please see my further 
>> comments/questions below in UPPER:
>>
>> xps uses the "most proper" pgf and bkg Affymetrix annotation
>>
>> SO THESE WOULD BE WHATEVER AFFYMETRIX IS PROVIDING - NOT REMAPPED 
>> FILES, CORRECT? IF YOU'RE FAMILIAR WITH XPS, COULD YOU INDICATE WHERE 
>> IN THE DOCUMENTATION THE INITIAL PROCESSING OF EXON ARRAYS (WITH 
>> REFERENCE TO THE USE OF PGF AND BKG) IS MENTIONED.
>>
>> , while exonmap gives you
>> more flexibility of playing around with annotations
>>
>> I REALIZE THAT XMAP HAS REMAPPED FILES
>>
>> - both require extra database installation
>> effort, but I think it is worth it.
>>
>> Did you run the summarization with this package?
>>
>> I RUN THE COMPLETE RMA 'PROCESSING' SO THAT INCLUDED SUMMARIZATION.
>>
>> I think the discussion in Oct 07 was about
>> the fact that you have to remove some probesets to run RMA... or was 
>> it fixed?
>>
>> I COULD NOT TELL FROM THE COMMUNICATION IF THAT WAS FIXED. BECAUSE I 
>> HAD NO ISSUES RUNNING RMA USING THIS CDF PACKAGE, WOULD LIKE TO ASK IF 
>> THE AUTHOR OF huex10stv2cdf_1.15.0.tar.gz HAVE FIXED IT
>>
>> You can use also the CDFs from X:MAP downloads page - they manage with 
>> RMA/plier.
>>
>> I WAS CONSIDERING THAT, BUT WASN'T SURE IF I'LL STILL NEED THE DB 
>> SETUP FOR GETTING THE 'REMAPPED' ANNOTATION, OR WHETHER I COULD GET A 
>> FLAT FILE THAT I COULD USE TO ANNOTATE 'EXTERNALLY'.
>>
>> Cheers,
>> Dan
>>
>>
>> Michal Okoniewski wrote:
>>>
>>>
>>> -----Original Message-----
>>> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Dan Strumpf
>>> Sent: Mon 1/26/2009 10:17 PM
>>> To: bioconductor at stat.math.ethz.ch
>>> Subject: [BioC] use of huex10stv2cdf_1.15.0.tar.gz and human exon 
>>> array analysis
>>>  
>>> Hello,
>>>
>>> I am new to exon array analysis and have used the 
>>> huex10stv2cdf_1.15.0.tar.gz package (downloaded from 
>>> http://aurora.lbl.gov/static/huex10stv2cdf_1.15.0.tar.gz
>>> )as a cdf source/mapping for processing Human exon array data within 
>>> 'affy' package. Processing went smoothly without any error messages. 
>>> Noticed some communication about this package in Oct. 2007, and am 
>>> not clear if results using it are relaible.
>>> I am interested in processing Human exon array data also with gcRMA 
>>> and am wondering if should use the above package or use 
>>> xps/exonmap/oligo instead? Would like to know also what are to 
>>> options for differential expression analysis equivalent to samr limma 
>>> or RankProd for paired samples from within exon array analysis 
>>> packages or could the preprocessed/normalized data be exported and 
>>> used with xps/exonmap/oligo packages.
>>>
>>> Thanks,
>>>
>>> Dan
>>> =====================================================
>>>
>>> Hi Dan,
>>>
>>> xps uses the "most proper" pgf and bkg Affymetrix annotation, while 
>>> exonmap gives you
>>> more flexibility of playing around with annotations - both require 
>>> extra database installation
>>> effort, but I think it is worth it.
>>>
>>> Did you run the summarization with this package? I think the 
>>> discussion in Oct 07 was about
>>> the fact that you have to remove some probesets to run RMA... or was 
>>> it fixed?
>>> You can use also the CDFs from X:MAP downloads page - they manage 
>>> with RMA/plier.
>>>
>>> Cheers,
>>> Michal
>>
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>>
>