Athurva Gore/LabNotes/ExomeReseq/2009-5-13

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Revision as of 22:34, 13 May 2009 by >Ajgore (New page: =iPS Cancer?= * Obtained Illumina Array data from Dr. Zhang * Used SAM and DAVID to try and identify GO Terms in differentially expressed genes. * Say we want a desired FDR of 15% or lower...)
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iPS Cancer?

  • Obtained Illumina Array data from Dr. Zhang
  • Used SAM and DAVID to try and identify GO Terms in differentially expressed genes.
  • Say we want a desired FDR of 15% or lower; since we are just doing preliminary.
  • SAM's multiclass feature is not useful here; it will call everything that is fibroblast-only "significant," leading to numbers that are far too large.

Very Lenient

  • Very lenient analysis results in a large amount of GO Terms and GO Clusters.
  • Delta of 2.3 was used for IPS_HESC
  • Delta of 0.1 (very low, since figured a lot of genes would need to be called as "not similar")
  • Will upload DAVID results to Wiki.
  • Lots of very interesting GO terms and GO clusters
  • However, inspection of several reveals that these values may be too lenient. Lots of things are called as significant that are not very.

Very Stringent

  • Limited ESC_IPS differences to 475, limited GO differences to 250.
  • In this case, only 3 or 4 clusters were obtained at all (only 23 diff. expressed genes)
  • Most of them have very low scores...probably too stringent here

New Method

  • It seems SAM has issues finding differences between fibroblasts and IPS that are meaningful
  • Because so many genes are differentially expressed already, very hard to choose a proper delta value.
    • FDR is predicted to be very high.
  • Instead, will find differentially expressed genes between IPS and HESC first.
    • Only look at these in Fibroblasts, then run SAM!
  • Should help find any genes that do not match normal Fibroblasts or hESC in iPS cells.
  • Should help find some new behavior.