getMainProbes: Remove control probesets from ST arrays
In jmacdon/affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips
getMainProbes R Documentation
Remove control probesets from ST arrays
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 <jmacdon@u.washington.edu>
jmacdon/affycoretools documentation built on Nov. 2, 2024, 1:29 a.m.
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| getMainProbes | R Documentation |
Remove control probesets from ST arrays
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 <jmacdon@u.washington.edu>
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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