RMAExpress protocols

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RMAExpress specifications

Information


Unique identifier OMICS_25090
Name RMAExpress
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.20.0-alpha-4
Stability Alpha
Maintained Yes

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  • person_outline Benjamin Bolstad <>
  • person_outline Benjamin Bolstad <>

Publication for RMAExpress

RMAExpress in pipelines

 (6)
2015
PMCID: 4430867
PMID: 25948104
DOI: 10.1186/s12885-015-1337-3

[…] each study, data obtained from sensitive and resistant cell lines were saved in different columns of excel spread sheets. datasets obtained from affymetrix studies were combined and analyzed using rmaexpress for quality control [,]. for non-affymetrix studies, where we could not run rmaexpress quality control, we downloaded already normalized, _raw.tar files and used these without […]

2015
PMCID: 4604084
PMID: 26462087
DOI: 10.1371/journal.pone.0140022

[…] the affymetrix genetitan mc scanner (affymetrix inc.) with default settings. quality control of the microarray data was performed using oligo (oligo bioconductor package)[] and rma express (http://rmaexpress.bmbolstad.com/)[]. factor analysis for robust microarray summarization (farms bioconductor package) [] was used to background correct, normalize, and summarize the data and filter […]

2015
PMCID: 4758289
PMID: 26497545
DOI: 10.3892/mmr.2015.4442

[…] data were subjected to background correction, normalization, probe summary and log2 logarithmic transformation using the robust multi-array average (rma express; version 1.0; http://rmaexpress.bmbolstad.com) method (). when several probes were found to project to one gene, the average was used to represent the expression levels of this gene. there were 27,342 probes in the raw […]

2013
PMCID: 3608085
PMID: 23391100
DOI: 10.1186/1471-2164-14-85

[…] files have been deposited in the gene expression omnibus (geo) database (pending). to compare data from multiple arrays, the signal of each probe array was scaled to the same target intensity value. rmaexpress [] was used for background adjustment, quintile normalization, summarization and quality analysis. regulated genes were selected as differentially expressed 50% […]

2013
PMCID: 3655826
PMID: 23663499
DOI: 10.1186/1471-2164-14-325

[…] maintaining of such a high-quality database. we also want to thank the open source bioinformatics community, particularly the yass team, the vienna rna group, the panther group, the gsea group, the rmaexpress team, the cluster team, and the treeview team. their excellent bioinformatics tools endow enormous values to the entire scientific […]


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RMAExpress in publications

 (105)
PMCID: 5913134
PMID: 29686383
DOI: 10.1038/s41467-018-03886-6

[…] array images were determined on the basis of background values, percent present calls, scaling factors, and 3’/5’ ratio of β-actin and gapdh. data were extracted from cel files and normalized using rmaexpress (http://rmaexpress.bmbolstad.com/) and annotated using mev software (http://www.tm4.org/mev.html). differentially expressed genes between different conditions were determined using a fold […]

PMCID: 5867872
PMID: 29518046
DOI: 10.3390/genes9030151

[…] and transcripts, was used for genome-scale networks analysis. the 90 array expression profiles included 84,286 probes, which were normalized with the robust multiple-chip analysis (rma) algorithm by rmaexpress []. the inferred network included 41,841 genes and 8,631,218 links when a z-score threshold of 0.8, based co-expression network and spearman-based association methods, was used. […]

PMCID: 5908116
PMID: 29498212
DOI: 10.1111/jcmm.13544

[…] performed according to the affymetrix expression analysis technical manual (affymetrix, santa clara, ca, usa). cel file normalization was performed with the robust multichip average method using rmaexpress (version 1.0.5) and the human entrez‐gene custom cdf annotation from brain array version 18 (http://brainarray.mbni.med.umich.edu/brainarray/default.asp). to identify differentially […]

PMCID: 5831110
PMID: 29489886
DOI: 10.1371/journal.pone.0193098

[…] fingerprint for each individual file and duplicate cel files will have an identical md5 hash. after removal of duplicate cel files, pre-processing and aggregation of cel files was performed with rmaexpress (version 1.1.0) by applying the robust multi-array average (rma) algorithm, using the latest affymetrix genechip array cdf layout files ref. principal component analysis (pca) […]

PMCID: 5659845
PMID: 29078207
DOI: 10.1371/journal.pone.0186386

[…] rnai against sbp-1 and sams-1 (gsm1816551-gsm1816559) []. the corresponding cel-files were obtained from the geo repository []. expression values were extracted and normalized with rmadataconv and rmaexpress []. similarly we obtained the cel-files and result files for the response of n2 nematodes to pathogenic bacteria, in particular to the vibrio cholerae strains vc109 and vc110 (gse34026) [] […]


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RMAExpress institution(s)
Group in Biostatistics, University of California, Berkeley, CA, USA; Department of Biostatistics, John Hopkins University, Baltimore, MD, USA; AstraZeneca R & D Molndal, Sweden; Department of Statistics, University of California, Berkeley, CA, USA; Division of Genetics and Bioinformatics, WEHI, Melbourne, VIC, Australia

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