MADMAX specifications

Information


Unique identifier OMICS_01006
Name MADMAX
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Database management system Oracle
Computer skills Advanced
Stability Stable
Maintained No

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Publication for MADMAX

MADMAX in publications

 (26)
PMCID: 5785967
PMID: 29374228
DOI: 10.1038/s41598-018-20068-y

[…] transcript sense target assay and hybridized to human whole-genome affymetrix gene 1.1 st arrays targeting 19697 unique genes (affymetrix, santa clara, ca). microarray analyses were performed using madmax pipeline for statistical analysis of microarray data. in short, microarrays were normalized with the robust multichip average method and probes were annotated as described,. this gene set […]

PMCID: 5847878
PMID: 29266667
DOI: 10.1111/acel.12696

[…] dix  for details). hybridization, washing, and scanning of affymetrix genechip mouse gene 1.1 st arrays were performed according to standard affymetrix protocols. microarray analysis was performed in madmax, a pipeline for statistical analysis of microarray data (lin et al., ). arrays were normalized using the robust multiarray average method (bolstad, irizarry, åstrand, & speed, ; irizarry et […]

PMCID: 5703654
PMID: 28987381
DOI: 10.1016/j.taap.2017.09.023

[…] been deposited in ncbi's gene expression omnibus (http://www.ncbi.nlm.nih.gov/geo/) and are accessible through geo series accession number gse102016., microarray analysis was performed using the madmax pipeline for statistical analysis of microarray data (). briefly, microarrays were normalized with the robust multichip average method and probes were annotated according to dai et al. (, ). […]

PMCID: 5687563
PMID: 29116234
DOI: 10.1038/s41477-017-0035-3

[…] gene 1.1 st 24-array plates (atlas) or single array strips (nuclear vs. cellular rna) (affymetrix, ca, usa) according to the manufacturers protocol. microarray analysis was performed using the madmax pipeline and a custom cdf file (mbni customcdf version 19.0.0). here, all expression values were (quantile) normalised by the robust multi-array average algorithm (rma) using the median polish […]

PMCID: 5665945
PMID: 29093568
DOI: 10.1038/s41598-017-14926-4

[…] genes (affymetrix, santa clara, ca). sample labelling, hybridization to chips and image scanning was performed according to the manufacturer’s instructions., microarray analysis was performed using madmax pipeline for statistical analysis of microarray data. quality control was performed and all arrays met our criteria. for further analysis a custom annotation was used based on reorganized […]


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MADMAX institution(s)
Laboratory of Bioinformatics, AN Wageningen, Netherlands; Laboratory of Plant Breeding, Wageningen, Netherlands; RIKILT, Wageningen, Netherlands; Nutrition, Metabolism and Genomics Group, Wageningen, Netherlands; Netherlands Bioinformatics Centre (NBIC), Nijmegen, Netherlands; Institute of Vegetable and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China

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