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Exon Array Analysis

Frequently Asked Questions

  1. How big are the .dat and .cel files?

  2. What are the basic quality assessment metrics for the Exon Array?

  3. Can I compare the Signal value between two exons directly to obtain a ratio of two different transcripts?

  4. What analysis software packages are available for Exon Array data analysis?

  5. Can I compare Exon Array results with those obtained on the GeneChip® Human Genome U133 (HG-U133) Array?

  6. How long will it take for me to analyze the data?

  7. What can I do to reduce the analysis time required to generate probe set level signal?

  8. What is DABG, PLIER?

  9. Can I get gene-level expression results?

  10. How do I correlate the SNPs on the mapping array with this design?

  11. When I loaded the exon array design information and array data into IGB, it seems that the probes were selected from outside of the RefSeq exons. Why?

  12. How do you move the .cel files out of GCOS to be imported into Expression Console?

  13. Two alternative splicing detection methods were described in the white papers from the Affymetrix web site. Are they related to the ANOSVA SVD algorithm that was published in Bioinformatics in 2005 by Cline, et al?

  14. Is there an option to view the various types of annotation information from NetAffx™ Analysis Center in IGB so you can combine the textual annotation with visualization?

  15. Is it possible to launch IGB as a stand alone program without having the machine networked? I know that it could be done once the data are acquired but could I do it right from the beginning, just opening IGB and loading a file locally?