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

[Dan Strumpf]

Hi Jim,

Thanks for your reply and insight. I will check out your suggestions, 
and evaluate to best strategy for generating the expression data set and 
then analysing it 'externally'.

Best,

Dan

James W. MacDonald wrote:
> Hi Dan,
> 
> Dan Strumpf wrote:
>> 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 don't know anything about that cdf, but if it is similar to the 
> modified cdf that you can get from PICR for exonmap, you should get 
> pretty much the same values, as exonmap uses the affy package and a 
> modified cdf to compute expression values.
> 
> The upside to using exonmap is that you have ways to map the probesets 
> to their location on the genome, and could thereby filter out those that 
> hit what are considered to be inter-genic or intronic positions.
> 
> I don't know if you will be able to use gcrma, as there are no MM probes 
> on the exon chips. Instead they just have two sets of probes that are 
> designed to measure background.
> 
> 
>> 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.
> 
> Pre-processing and differential expression are in general handled by 
> different packages. For instance, you don't use the affy or gcrma 
> package to look for differentially expressed genes, and the same holds 
> true for xps, exonmap, and oligo.
> 
> That said, there isn't really that much different between the exon chip 
> data and the 3' biased arrays, so tools like limma and RankProd should 
> be fine for analyzing these data.
> 
> Best,
> 
> Jim
> 
> 
>>
>> Thanks,
>>
>> Dan
>>
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>