User:Diego Forero/Notebook/Silico-Meta/2009/09/19

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Details for Tools

RankProd; Hong 2006

  • Based in Breitling 2004
  • Non-parametric-rank based, consistently highly ranked, ranking products
  • INPUT: Matrix: Gene expression; Vector: Class labels; Vector: Origins; Vector: GeneNames
  • Calculation of rank products, Permutation, calculation of FDR
  • OUTPUT: Overview of general results for up and down.

Table with Gene, FC, FDR, P, for up and down

  • Use with affymetrix, also with cDNA data; single origin or multiple origins
  • Notes: Web based tool?, Different platforms, only genes in common?

GeneMeta; Gentleman 2009

  • Based in Choi JK, 2003
  • size effect (t test);
  • INPUT: ExpressionSet format
  • random effects model (REM) and fixed effect model (FEM)
  • OUTPUT: Overview of general results for up and down.

Table with probe, P, size effect, Graph with FDR

  • Use with affymetrix or other two channels
  • Notes: Different platforms, only genes in common?

Identification of most significant genes?

OrderedList; Lottaz 2006

  • Based in Yang X, 2006
  • similarities between ordered gene lists;
  • INPUT: ExpressionSet format or ordered gene lists
  • similarities between ordered gene lists
  • OUTPUT:Significance of similarity, most significant genes

Plots of general similarities

  • Use with affymetrix or with single channel
  • Notes: Different platforms, only genes in common?

I made the graph about the relative growth of publications and data about microarray experiments.

  • Papers about microarrays (Red, X100); microarrays and meta-analysis (Blue, X1); meta-analysis (Green, X100); all papers in PubMed (Black, X10.000). Number of microarray hybridizations available in ArrayExpress database (Gray, X10.000) and submissions to NCBI GEO database (Magenta, X10.000).
  • I posted it online:
  • It seems that the growth in papers about meta-analysis parallels the general trends of growth of PubMed. On other hand, it is clear the fast growth of papers about microarrays. Papers about meta-analysis of microarrays also show an accelerated growth in recent years.There is only data about growth of ArrayExpress database from 2004. Content of NCBI GEO is larger.

I sent an email to Dr Barrett asking about the availability of statistics related to the growth in the content of NCBI GEO in last years. I received an answer from her and an excel files with statistics from Jan 2001. I updated the graph.