Re: C. elegans tiling array analysis

[Nathan Salomonis]

Hi Julian,

AltAnalyze has not been evaluated for use with genome tiling arrays, only transcriptome. 

AltAnalyze typically supports two kinds of analyses; 1) Analysis of all probesets in an unbiased way and 2) analysis of exon and junction expression data according to an Ensembl gene model. 

For CEL file analysis, AltAnalyze downloads or accepts CDF or PGF/CLF/BGP library files. Other libraries are not currently used. It appears that tiling arrays use additional library files that are not used with the current pipeline. Although it could accept RNA expression data for gene expression and splicing analyses for any species in the form of an exon.bed file, the analysis will be focused on known genes. For more info on this, see:

http://code.google.com/p/altanalyze/wiki/SplicingForAnyPlatform

What are your goals for the analysis of this data?

Best,

Nathan

On Feb 6, 2012, at 4:31 AM, Julian Ceron Madrigal <jceronm...@gmail.com> wrote:

Hi Nathan
I tried to use Altanalyze to analyze CEL files from a C. elegans tiling arrays from affymetrix (see link below),. but it seem that i doesn't work.
Do you know if I could use your software to perform this analysis?

http://www.affymetrix.com/estore/browse/products.jsp?navMode=34000&productId=131424&navAction=jump&aId=productsNav

Thanks for yor help,
julián
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<image001.jpg>   Julián Cerón Madrigal PhD Genetics and Functional Genomics in C. elegans Cancer and Human Molecular Genetics Area Hospital Duran i Reynals 3a planta - Gran Via de l'Hospitalet, 199 08908 L'Hospitalet de Llobregat Barcelona – Spain   Tel : +34 93 260 72 51 jceron@idibell.cat  www.idibell.cat www.gusano.info   Avís legal - Aviso legal - Legal notice