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: 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.
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.
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