.mIRIS. CellMix 1.6

Description

CellMix access key: “IRIS”

List of marker probesets for immune cell types from the IRIS dataset (Abbas et al. (2005)). It contains Affymetrix probesets of markers for B cells, dendritic cells, monocytes, neutrophils, NK cells and T cells, as well as for the lymphoid and myeloid lineages, and the general category of all these immune cells.

Usage

.mIRIS(id = c("AFFY", "ENTREZID", "ENSEMBL"), score = "F", threshold = 0)

Arguments

id: original identifier to use.
score: name of the column from the IRIS dataset to use as a score.
threshold: minimum value threshold for filtering on scores.

Source

http://share.gene.com/clark.iris.2004/iris/iris.html

Details

The MarkerList object is generated by the internal function .mIRIS, to which arguments can be passed via MarkerList('IRIS', ...) to build lists, using different original identifiers and filtering threshold.

However, it is recommended to rather use the function convertIDs to convert the primary identifiers into other identifiers, using up-to-date annotation packages.

The markers are ordered in each cell type by decreasing F value (from fData(IRIS)$F), i.e. from the more to the less cell type-specific.

References

Abbas AR, Baldwin D, Ma Y, Ouyang W, Gurney A, Martin F, Fong S, van Lookeren Campagne M, Godowski P, Williams PM, Chan aC and Clark HF (2005). "Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data." _Genes and immunity_, *6*(4), pp. 319-31. ISSN 1466-4879, , .