getMainProbes: Remove control probesets from ST arrays

In affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Description

This function is designed to remove all but the 'main' type of probesets from the Gene ST array types.

Usage

getMainProbes(input, level = "core")

Arguments

input	Either a character string (e.g., "pd.hugene.1.0.st.v1") or a FeatureSet object.
level	The summarization level used when calling rma.

Value

If the argument is a character string, returns a data.frame containing probeset IDs along with the probeset type, that can be used to subset e.g., an ExpressionSet of Gene ST data, or an MArrayLM object created from Gene ST data. Note that the order of the probesets is not guaranteed to match the order in your ExpressionSet or MArrayLM object, so that should be checked first. If the argument is a FeatureSet object, it returns a FeatureSet object with only main probes remaining.

Author(s)

James W. MacDonald <[e-mail]>

affycoretools documentation built on Nov. 8, 2020, 6 p.m.