MEAP specifications

Information


Unique identifier OMICS_11341
Name MEAP
Alternative name Multiple Exon Array Preprocessing
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Biological technology Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Parallelization MPI
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.1
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Ping Chen <>

Publication for Multiple Exon Array Preprocessing

MEAP in publications

 (6)
PMCID: 5596382
PMID: 28841210
DOI: 10.1038/bcj.2017.71

[…] data are available at arrayexpress archive (http://www.ebi.ac.uk/arrayexpress/experiments/e-mexp-3488). gene- and exon-level expression data for the nlg-lbc-04 discovery cohort were quantified by meap (multiple exon array preprocessing) algorithm with meap probe annotation version 70., in the cgci validation cohort, adaptors and low-quality bases were trimmed from the samples […]

PMCID: 5444266
PMID: 26944083
DOI: 10.1093/bib/bbw016

[…] abundance from exon-array data. three such programs were tested on the tcga exon-array data: the multi-mapping bayesian gene expression (mmbgx) method [], the puma r/bioconductor package [] and the multiple exon array preprocessing (meap) method []. each of these algorithms has shown better performance than two other popular tools, piler and rma, in their respective studies. furthermore, […]

PMCID: 4430308
PMID: 25970770
DOI: 10.1371/journal.pone.0124931

[…] hippocampi of five control and five ethanol-exposed four-week-old male offspring (from two and three litters, respectively)., the exon array probe expression values were normalized first with the meap algorithm [], [], [] followed by background and noise corrections. the normalized probe signals were transformed into gene expression values using meap. the analysis was done in the freely […]

PMCID: 4432789
PMID: 25958224
DOI: 10.1186/s12920-015-0094-0

[…] including relative log expression (rle), positive vs. negative roc auc and mad-residual mean, were all within the parameters suggested by affymetrix., raw intensity data were processed using multiple exon array preprocessing (meap) software. the pm-bayesbg method was used for background correction. this was followed by quantile normalization, expression summarization and log2 […]

PMCID: 3953211
PMID: 24625556
DOI: 10.1371/journal.pone.0091031

[…] to genomic locus was counted. genes with more than 10 cnvs were excluded from the subsequent analyses. exon array expression data were normalized and transformed to gene expression level data by the multiple exon array preprocessing (meap) algorithm ., in order to find genes with a significant association of expression and cna, all genes in the expression data, which were located in a minimal […]


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MEAP institution(s)
Research Programs Unit, Genome-Scale Biology and Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki, Finland; Research Programs Unit, Molecular Cancer Biology Program and Haartman Institute, University of Helsinki, Finland
MEAP funding source(s)
Academy of Finland (grant number 125826), Biocentrum Helsinki; Finnish Graduate School in Computational Sciences; the Finnish Cancer Society; Sigrid Jusélius Foundation

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