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A SURVEY OF AVAILABLE COMPUTATIONAL TOOLS FOR META-ANALYSIS OF MICROARRAY EXPRESSION STUDIES
I am planning to write a paper describing the comparison of available tools for meta-analysis of microarray studies. This idea appeared as part of the plans for the meta-analysis of microarray data from post-mortem brains for AD and PD.
I searched in PubMed, Google Scholar and in the extended lists of R and Bioconductor for packages for meta-analysis of microarray studies. I found 10 packages: BayesPoolMicro, GeneMeta, MAID, metaArray, metaGEM, metahdep, metaMA, OrderedList, RankAggreg and RankProd. I posted the basic list in a Google Sites webpage: http://sites.google.com/site/compgensite/meta
MAID and metaGEM are not available in R or bioconductor. I have a local copy of metaGEM, previously sent by the author. GeneMeta is not described as a paper. I wrote an email to the authors of MAID and metaGEM to ask for their availability (firstname.lastname@example.org and Ian.McGilvray@uhn.on.ca) and to the authors of GeneMeta about plans for publishing a paper about it. Dr Ramasamy answered informing that he will try to have the package in Bioconductor soon. I received a copy of MAID from the authors.
I wrote a possible title and abstract for the paper
I sent a presubmission enquiry to the editor of 6 journals:
Dear Editor, we are working in molecular genetics and genomics of human disorders and we have published a number of papers in this area (Forero DA, J Neural Transm 2006; Forero DA, Neurosci Res 2006; Forero DA, Arch Med Res 2006; Forero DA, J Cell Mol Med 2006; Forero DA, J Psychiatry Neurosci, 2009). We have finished a manuscript describing a comparison of the features of eight available computational tools for meta-analysis of microarray data. We would like to know if this manuscript could be of interest for your journal. We are attaching the abstract at the end of the message. Thanks for your attention. Sincerely. Diego Forero, MD//Neurosciences Research Group//MSc Program in Neurosciences//Institute of Genetics-School of Medicine//National University of Colombia//Bogotá, Colombiaemail@example.com// Editor, hum-molgen.org
Dear Dr Forero, Thank you for agreeing to submit the manuscript entitled "A SURVEY OF AVAILABLE COMPUTATIONAL TOOLS FOR META-ANALYSIS OF MICROARRAY EXPRESSION STUDIES" to Briefings in Bioinformatics. Please try your best to submit this manuscript within the next 30 days. To access the manuscript, login to Briefings in Bioinformatics - Manuscript Central site at http://mc.manuscriptcentral.com/bib. Once you are logged in, the Main Menu will be displayed. Please click on the Author Center, where you will find the manuscript listed under "Invited Manuscripts." You can click on the "Continue Submission" button to begin manuscript submission. All communications regarding this manuscript are privileged. Any conflict of interest must immediately be reported to me. Thank you for agreeing to submit this manuscript. Yours sincerely, Alison Bentley. Briefings in Bioinformatics Editorial Office. firstname.lastname@example.org
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THINGS TO DO:
search "microarray*"// search "microarray* and meta-analysis"// years 1996-2008
Use or not of a previously available tool for meta-analysis
Number of citations (Google Scholar). Number of downloads (Bioconductor). Number of citations for method paper. Type of inputs. Type of methods implemented. Type of outputs. Additional comments.
2 different datasets (3 studies for each one): 10 samples, 1000 probe datapoints.// 20 samples, 1000 probe datapoints.// To describe: Processing time, outputs, consistency between tools.
PMC2582039 PMC2515154 PMC2495035 PMC1458884 PMC1904223 PMC2275244 PMC2743637 PMC1664699 PMC2642844 PMC1180834 PMC2098839 PMC2640456 PMC2444034 PMC1273632 PMC1906587 PMC1636648 PMC1853113 PMC2650420 PMC2716681 PMC2525640 PMC1716187 PMC2633354
Further details (and active links) are given in http://sites.google.com/site/compgensite/meta-applied