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

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Details for Tools
- RankProd; Hong 2006 Table with Gene, FC, FDR, P, for up and down -
 * 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.
 * 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

Identification of most significant genes?
 * Use with affymetrix or other two channels
 * Notes: Different platforms, only genes in common?

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OrderedList; Lottaz 2006

Plots of general similarities
 * 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


 * 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. 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. -
 * 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: http://sites.google.com/site/compgensite/dynamics
 * 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.


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