getDatasets: Get datasets in ExpressionSet format

Description Usage Arguments Value References Examples

Description

Get the datasets for every platform for the given dataset identifier.

Usage

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getDatasets(dataset, ...);

Arguments

dataset

Valid dataset identifier: the GEO or InSilico DB accession code.

...

Optional arguments can be passed to the function for more specific requests:

format = "CURESET"

File format in which the dataset should be returned. Possible values:

  • CURESET : Curated R/Bioconductor ExpressionSet.

  • ESET : R/Bioconductor ExpressionSet without curation.

features = "PROBE"

Type of features in which data is represented. Two possible values: "GENE" or "PROBE". By default an expression matrix containing probes is returned

norm = "ORIGINAL"

Type of normalization to use when pre-processing a dataset. Possible normalizations: "ORIGINAL", "FRMA"[1], "SCAN"[2].

curation

Specific curation used to annotate a dataset. A curation is identified by a InSilico DB Curation identifier. You can annotate datasets yourself at https://insilicodb.com/app/browse If not defined, the default curation of specified dataset will be used.

timeout = 120

Time (in seconds) to wait for the dataset, if it has to be generated.

Value

A list with a Bioconductors ExpressionSet for every platform.

References

[1] MN. McCall, BM. Bolstad, and RA. Irizarry, Frozen Robust Multi-Array Analysis (fRMA), Biostatistics, vol. 11, no. 2, pp. 242-253 , 2008.

[2] SR. Piccolo, Y. Sun, JD. Campbell, ME. Lenburg, AH. Bild, and WE. Johnson, A single-sample microarray normalization method to facilitate personalized-medicine workflows, Genomics, vol. 100, no. 6, pp. 337-344, 2012.

Examples

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InSilicoLogin("[email protected]", "5c4d0b231e5cba4a0bc54783b385cc9a");
dataset.id <- "GSE1456"
getPlatforms(dataset.id);
## [1] "GPL96" "GPL97"
esets <- getDatasets(dataset.id, norm = "ORIGINAL");
sapply(esets, annotation)
##    GPL96    	 GPL97
##    "hgu133a"   "hgu133b"

inSilicoDb documentation built on Oct. 5, 2016, 4:40 a.m.