[BioC] Human Gene array data analysis workflow

[Moshe Olshansky]

I personally would not remove control transcripts before looking for
differential expression, since they may serve as a negative control, i.e.
if many of them are differentially expressed between samples it means that
something is wrong (or at least suspicious).

Best regards,
Moshe.

> Dear list,
> A possible data analysis workflow for EXON arrays could be as follows
> (extracted from "Exon Array data analysis using Affymetrix Power Tools
> and R statistical software", Briefings in Bioinformatics):
>
>     * Normalization and summarization (at exon or gene-level) of the
>       array set.
>     * Quality control of exon array data of summarization results (to
>       remove possible outliers)
>     * Specific filtering steps, for example:
>           o Restrict analysis to core probesets
>           o Filter for undetected probesets (i.e., undetected exons),
>             making use of DABG (Detected above background) analysis.
>           o Filter for cross-hybridizing probesets (exons)
>           o Filter for genes undetected genes in all groups
>
>   I'm running a gene-level data analysis on Human GENE ST 1.0 (not EXON)
> arrays, which are, in principle, designed for gene expression profiling,
> that is, a gene-level analysis. My question is related to the filtering
> step. I was wondering if, once the normalization and summarization is
> run at the transcript level (core), giving 33297 transcripts, the
> following filtering can be run before differential expression analysis:
>
>     * Remove control transcripts such as other_spike, AFFX, pos_control
>       (normgene->exon) and neg_control (normgene->intron). This step
>       removes around 4156 transcripts
>     * Remove transcripts with very low variability through varFilter
>       function (genefilter package)
>
> Since these were the steps recommended in "Bioconductor case studies"
> book for 3'IVT arrays (the controls were different in 3'IVT), I was
> wondering if these 2 filtering steps can also be used on Human Gene
> arrays for gene-level analysis or, on the contrary, I have to run the
> filtering steps described above for EXON arrays.
> Thanks,
> Javier
> P.S. If you know any data analysis workflow document for HuGene arrays,
> please, let me know
>
> 	[[alternative HTML version deleted]]
>
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-- 
Moshe Olshansky
Division of Bioinformatics
The Walter & Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Vic 3052
e-mail: olshansky at wehi.edu.au
tel: (03) 9345 2697


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