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Protocols

SAM specifications

Information


Unique identifier OMICS_00779
Name SAM
Alternative names Significance Analysis of Microarrays, samr
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Significance_analysis_of_microarrays

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Documentation


Publication for Significance Analysis of Microarrays

SAM citations

 (1196)
library_books

Robust volcano plot: identification of differential metabolites in the presence of outliers

2018
BMC Bioinformatics
PMCID: 5896081
PMID: 29642836
DOI: 10.1186/s12859-018-2117-2

[…] i) classical parametric approaches, such as Student’s t-test [], classical volcano plot (CVP) [] and fold change rank ordering statistics (FCROS) [], (ii) classical non-parametric approaches, such as significance analysis of microarrays (SAM) [], and the Wilcoxon [] and Kruskal-Wallis (K-W) [] tests, (iii) Bayesian parametric approaches, such as Bayesian robust inference for differential gene expr […]

library_books

Neutralizing Anti Cytokine Autoantibodies Against Interferon α in Immunodysregulation Polyendocrinopathy Enteropathy X Linked

2018
Front Immunol
PMCID: 5885158
PMID: 29651287
DOI: 10.3389/fimmu.2018.00544

[…] Heat maps were generated and significance analysis of microarrays (SAM) performed using the free software Multiple Experiment Viewer (, ). SAM false discovery rates (FDR) were set to <0.001.Indirect immunoassay results were teste […]

library_books

Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer

2018
Sci Rep
PMCID: 5871839
PMID: 29593348
DOI: 10.1038/s41598-018-22488-2

[…] We used the R software package for statistical analyses. We used the prcomp package for PCA analysis and the samr package for the Significance Analysis of Microarrays. Plots were generated using the gplots, matplotlib and igraph packages. […]

call_split

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

2018
Front Plant Sci
PMCID: 5881139
PMID: 29636762
DOI: 10.3389/fpls.2018.00384
call_split See protocol

[…] rizarry, ). Arrays were normalized using quantile normalization (Bolstad et al., ) and probeset summarization used median polish (Berger and Carlon, ). Arrays were analyzed for significance using the Significance Analysis of Microarrays test (Tusher et al., ), and probesets with a p-value ≤ 0.05 and at least 2-fold change of their log values were retained for further analysis. Gene annotations for […]

call_split

Identification of p38 MAPK as a novel therapeutic target for Friedreich’s ataxia

2018
Sci Rep
PMCID: 5864720
PMID: 29568068
DOI: 10.1038/s41598-018-23168-x
call_split See protocol

[…] ssion levels of targeted genes, RMA normalization was applied using Partek Genomics Suite v6.6, yielding log2-transformed normalized intensities. Genes were analyzed for differential expression using Significance Analysis of Microarrays (SAM; samr v2.0). The gene list was then sorted by q values, a statistical parameter that takes into account the magnitude of the differences, the precision of the […]

library_books

Benchmarking common quantification strategies for large scale phosphoproteomics

2018
Nat Commun
PMCID: 5849679
PMID: 29535314
DOI: 10.1038/s41467-018-03309-6

[…] SAM analysis was performed either in R with the R package SAMR v2.0 (two class paired or unpaired t-testing, automatic s0 and FDR-based delta-determination, a random seed = 123, and default values or otherwise indicated for the FDR), or in Perseus v1.6.0.7 ( […]

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SAM institution(s)
Departments of Medicine and Biochemistry, Stanford University, Center for Clinical Sciences Research, CA, USA; Department of Health Research and Policy and Department of Statistics, Stanford University, Stanford, CA, USA
SAM funding source(s)
Supported by the Burroughs Wellcome Clinical Scientist Award and by National Institutes of Health (NIH)Grant CA77302, NIH Small Business Technology Transfer grant CA75675, Affymetrix, and by the Stanford Genome Training Grant.

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