Output Files with different gene lists

[Ana R. Grosso]

Hi

I have analyzed exon-array data with AltAnalyze and I have found
different gene lists when checking the output files. I could not find
any explanation in your manual.
Per example, at gene level:
- ExpressionOutput/DATASET-project.txt - 1446 genes (rawp.old_vs_young
< 0.05 );
- ExpressionOutput/GenMAPP-project.txt - 2875 genes (rawp.old_vs_young
< 0.05 );

I found the similar weird result for alternative splicing:
- AltResults/AlternativeOutput/Hs_Exon_A_vs_B.p5_average-FIRMA-exon-
inclusion-results.txt - 523 genes
- AltResults/AlternativeOutput/Hs_Exon_A_vs_B.p5_average-FIRMA-exon-
inclusion-GENE-results.txt - 663 genes
How can a gene appear in GENE level organized list and not be present
in the total list of events?

Thank you
Ana Grosso

[Nathan Salomonis]

Hi Ana,

I have the feeling that you have two separate analyses or runs that are clobbering each other, but I haven't heard of this before. Indeed, all the same statistics are represented in the DATASET and GenMAPP results and the gene level alternative exon results are summarized at the gene level proving less results (all same genes). I just verified this with a few datasets. I recommend moving your input files CEL files to a new directory and re-running the analysis. For simplicity, run only one pairwise group comparison.

Best,
Nathan

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[Nathan Salomonis]

Forwarded from user:

---------------------------

I was checking the results with R and some lines were being "commented". 

I tried now to open the output files using the options (quote="", comment.char="") and the results are consistent.

Thank you for your help.

Congratulations for the great tool!

Ana

End Quoted Text

On Mar 16, 2012, at 9:39 AM, "Ana R. Grosso" <anarit...@gmail.com> wrote: