SAM pipeline

SAM specifications


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



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  • person_outline Gilbert Chu <>

Publication for Significance Analysis of Microarrays

SAM IN pipelines

PMCID: 4892488
PMID: 27257970
DOI: 10.1371/journal.pone.0156006

[…] if present in at least 50% of samples in any group using r bioconductor affy package [23]. after the initial filtering, 17,310 genes were left. the data set was preprocessed further by applying significance analysis of microarrays (sam) [24] to remove genes that show no or very low changes in expression between healthy and disease samples, but also for the purpose of getting manageable size […]

PMCID: 5398387
PMID: 27488871
DOI: 10.4143/crt.2016.080

[…] and pre-processing of the array data, including log2 transformation, differential gene expression analysis of pbmc samples taken before and after vorinostat administration was conducted using the significance analysis of microarrays algorithm and by applying the setting of paired-comparisons with a false discovery rate of 5% [21]. cluster analysis of the differentially expressed genes […]

PMCID: 4360913
PMID: 25793155
DOI: 10.1016/j.gdata.2015.02.002

[…] .gene[,3:6],2,mean_gene_value)write.table(con.test.meangene,file =“siggenes.txt”,sep =“\t”,row.names=true, quote=false)dim(con.test.meangene), normalization, library(affy), library(siggenes), library(samr), library(annotate), library(hgu133plus2.db), library(gplots), get.gene<-function(row), row<-unlist(row), genename<-get(row[1], hgu133plus2symbol), return (genename), ttest.row<-funct […]

PMCID: 3664306
PMID: 23603793
DOI: 10.1038/ni.2576

[…] quantile normalize fluorescent hybridization signals using the robust multichip averaging method51. transcripts were then log2 normalized. differentially expressed genes were identified using the significance analysis of microarrays algorithm52 and network analysis was performed through the use of ipa (ingenuity systems, hierarchical clustering was performed with gene […]

PMCID: 3764031
PMID: 24040155
DOI: 10.1371/journal.pone.0074034

[…] normalization and cyclicloess. the quality of the outcome was assessed by different plots produced by the software package arrayqualitymetrics implemented in the r language. a supervised method (significance analysis of microarrays -sam-) [17] was then used to find the more significant (adjusted p<0.05) differentially expressed genes in rectal cancer patients who responded to treatment […]

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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