MergeMaid protocols

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MergeMaid statistics

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MergeMaid specifications

Information


Unique identifier OMICS_02124
Name MergeMaid
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.52.0
Stability Stable
Requirements
R(>=2.10.0), methods, Biobase, MASS, survival
Maintained Yes

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Publication for MergeMaid

MergeMaid in pipeline

2006
PMCID: 1557528
PMID: 16872493
DOI: 10.1186/1471-2407-6-200

[…] negligible intra-assay variation (≤5% cv) and low inter-assay variation (≤10% cv) when evaluated on raw linear expression quantities., meta-analysis of expression data was performed by using affy, mergemaid and genefilter libraries implemented in bioconductor []. statistical analyses were performed with r []. gene differential expression was considered significant with an α = 0.05 and p-value […]


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MergeMaid in publications

 (6)
PMCID: 5499209
PMID: 28561063
DOI: 10.1038/ncomms15107

[…] space in the training phase by filtering out all genes that proved to be irreproducible across the three analytical platforms considered (illumina, rna-seq, and affymetrix). to this end, we used the mergemaid r-package to calculate a gene reproducibility index called icor, which allows to identify genes that are reproducible across distinct data sets without relying on any phenotypic […]

PMCID: 3792024
PMID: 24116146
DOI: 10.1371/journal.pone.0076746

[…] affymetrix u133a and u133b), probe sets with higher mean expression values were selected if multiple probe sets mapped to same gene. the datasets were then merged based on gene symbol using the mergemaid package (http://astor.som.jhmi.edu/mergemaid) available through bioconductor []. the meta-analyses were carried out using the rankprod method [], a non-parametric statistical method, […]

PMCID: 3144884
PMID: 21818257
DOI: 10.1371/journal.pone.0021260

[…] in either direction from gene's median value, and when the percent of data missing or filtered out exceeded 50%. genes passing the filtering criteria from each dataset were intersected using the mergemaid package for the r environment (http://www.r-project.org) to identify common genes across multiple datasets. next, the “intcor” function of mergemaid was used to perform integrative […]

PMCID: 3046484
PMID: 21182765
DOI: 10.1186/gb-2010-11-12-r124

[…] regardless of the vast sample variations. the higher the absolute corcor value, the stronger correlation of the orthologous genes is; negative corcor indicates negative correlation. the r package mergemaid was used for this analysis []., corcor: correlation of correlation coefficient; go: gene ontology; pca: principal component analysis; plm: probe level model., the authors declare […]

PMCID: 2978933
PMID: 21082040
DOI: 10.4137/CIN.S5755

[…] platform and the choice for cross-referencing annotations was limited. we therefore mapped probes (or probesets) in each platform to unigene cluster identifiers (build 180) using the r package mergemaid. one-to-many mappings of probes to unigene clusters were excluded and many-to-one mappings were averaged., as sage can in theory detect the mrna transcripts for any gene, we only required […]


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MergeMaid institution(s)
The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, USA

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