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GC–RMA specifications


Unique identifier OMICS_29158
Alternative name gcrma
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Affymetrix
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.52.0
Stability Stable
methods, stats, graphics, Biobase, splines, utils, tools, XVector, R(>=2.6.0), affyio(>=1.13.3), BiocInstaller, affydata, hgu95av2probe, hgu95av2cdf, affy(>=1.23.2), Biostrings(>=2.11.32)
Maintained Yes




No version available



  • person_outline James MacDonald
  • person_outline Zhijin Wu

Publications for GC–RMA

GC–RMA citations


Pyoverdine, a siderophore from Pseudomonas aeruginosa, translocates into C. elegans, removes iron, and activates a distinct host response

PMCID: 5955448
PMID: 29532717
DOI: 10.1080/21505594.2018.1449508

[…] lean-up using an RNEasy kit (Qiagen). cRNA was prepared according to the manufacturer's protocol and hybridized to Affimetrix C. elegans GeneChip™ (Platform GPL200).Gene expression was analyzed using GCRMA (http://www.bioconductor.org). Differentially upregulated genes were determined on the basis of fold change compared to both controls (>3) and the value of a modified Wilcoxon rank test >1.5 aga […]


A Transcriptomic Analysis of Xylan Mutants Does Not Support the Existence of a Secondary Cell Wall Integrity System in Arabidopsis

Front Plant Sci
PMCID: 5881139
PMID: 29636762
DOI: 10.3389/fpls.2018.00384
call_split See protocol

[…] Data analysis was done using the R-based FlexArray software (Blazejczyk et al., ). For the background correction of raw data, Gene Chip—Robust Multi-array Analysis (GC-RMA) was used (Wu and Irizarry, ). Arrays were normalized using quantile normalization (Bolstad et al., ) and probeset summarization used median polish (Berger and Carlon, ). Arrays were analyzed f […]


Adjuvant Associated Peripheral Blood mRNA Profiles and Kinetics Induced by the Adjuvanted Recombinant Protein Candidate Tuberculosis Vaccine M72/AS01 in Bacillus Calmette–Guérin Vaccinated Adults

Front Immunol
PMCID: 5879450
PMID: 29632533
DOI: 10.3389/fimmu.2018.00564

[…] The raw microarray data were normalized via GeneChip-Robust Multiarray Averaging (GC-RMA) (), and outliers were excluded using the AffyPLM software package (open source; www.bioconductor.org, WA, USA) (–). For the PBMC samples, 4/54 microarrays were excluded, and for WB samples, 11 […]


Foxp1 controls mature B cell survival and the development of follicular and B 1 B cells

Proc Natl Acad Sci U S A
PMCID: 5866538
PMID: 29507226
DOI: 10.1073/pnas.1711335115
call_split See protocol

[…] was processed according to Affymetrix standard protocols and hybridized to the murine expression array MOE430 2.0 (Affymetrix). Expression data were processed in R by using the Bioconductor packages “gcrma” and “limma.” Genes differentially expressed at least log 1.5-fold in control vs. Foxp1-deficient cells were determined with a P value cutoff of 0.05 and Benjamini–Hochberg false discovery rate […]


GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6 LIKE 4 in Arabidopsis

PMCID: 5818008
PMID: 29439132
DOI: 10.1242/dev.159707
call_split See protocol

[…] scribed by . Total RNA was extracted from three biological replicates and labeled probes were used for hybridization on ATH1 chips (Affymetrix). Microarray data were analyzed using R software and the gcRMA implementation with AffylmGUI () of the Bioconductor package as previously described (; ). Microarray data have been deposited in Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) unde […]


Transcriptome dynamic of Arabidopsis roots infected with Phytophthora parasitica identifies VQ29, a gene induced during the penetration and involved in the restriction of infection

PLoS One
PMCID: 5744986
PMID: 29281727
DOI: 10.1371/journal.pone.0190341
call_split See protocol

[…] tome statistical analysis was performed as previously described []. After quality control with the Bioconductor package “simpleaffy” (Crisipn Miller), the cel-files were quantile-normalized with the “gcrma” package of Bioconductor []. Then, a quality control filter was performed. If the log2 ratios for the two time series differed by more than 75% of the mean of the two log2 ratios, the gene conce […]


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GC–RMA institution(s)
Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Dana-Farber Cancer Institute, Boston, MA, USA; Johns Hopkins Medical Institute, Baltimore, MD, USA

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