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

[cstrato]

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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