Class to contain and describe results of a differential expression (DE) analysis. The main components are statistic which hold the results of any statistic (e.g. p-values, PPLR values, etc.), and FC which hold the fold changes.
● Data Source:
BioConductor
● Keywords: classes
● Alias: DEResult, class:DEResult
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(Package: puma) :
Multi-chip modified gamma Model for Oligonucleotide Signal using only PM probe intensities
This function converts an object of class FeatureSet into an object of class exprReslt using the Multi-chip modified gamma Model for Oligonucleotide Signal (PMmulti-mgMOS). This method uses only PM probe intensites. This function obtains confidence of measures, standard deviation and 5, 25, 50, 75 and 95 percentiles, as well as the estimated expression levels.
● Data Source:
BioConductor
● Keywords: manip
● Alias: PMmmgmos
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bcomb
(Package: puma) :
Combining replicates for each condition
This function calculates the combined signal for each condition from replicates using Bayesian models. The inputs are gene expression levels and the probe-level standard deviation associated with expression measurement for each gene on each chip. The outputs include gene expression levels and standard deviation for each condition. This function was originally part of the pplr package. Although this function can be called directly, it is recommended to use the pumaComb function instead, which can work directly on ExpressionSet objects, and can automatically determine which arrays are replicates.
● Data Source:
BioConductor
● Keywords: manip, models
● Alias: bcomb
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calcAUC
(Package: puma) :
Calculate Area Under Curve (AUC) for a standard ROC plot.
Calculates the AUC values for one or more ROC plots.
● Data Source:
BioConductor
● Keywords: manip
● Alias: calcAUC
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calculateFC
(Package: puma) :
Calculate differential expression between conditions using FC
Automatically creates design and contrast matrices if not specified. This function is useful for comparing fold change results with those of other differential expression (DE) methods such as pumaDE.
● Data Source:
BioConductor
● Keywords: manip
● Alias: calculateFC
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1 images
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calculateLimma
(Package: puma) :
Calculate differential expression between conditions using limma
Runs a default analysis using the limma package. Automatically creates design and contrast matrices if not specified. This function is useful for comparing limma results with those of other differential expression (DE) methods such as pumaDE.
● Data Source:
BioConductor
● Keywords: manip
● Alias: calculateLimma
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1 images
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calculateTtest
(Package: puma) :
Calculate differential expression between conditions using T-test
Automatically creates design and contrast matrices if not specified. This function is useful for comparing T-test results with those of other differential expression (DE) methods such as pumaDE.
● Data Source:
BioConductor
● Keywords: manip
● Alias: calculateTtest
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1 images
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clusterApplyLBDots
(Package: puma) :
clusterApplyLB with dots to indicate progress
This is basically the clusterApplyLB function from the snow package, but with dots displayed to indicate progress.
● Data Source:
BioConductor
● Keywords: manip
● Alias: clusterApplyLBDots
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clusterNormE
(Package: puma) :
Zero-centered normalisation
This function normalise the data vector to have zero mean.
● Data Source:
BioConductor
● Keywords: manip
● Alias: clusterNormE
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clusterNormVar
(Package: puma) :
Adjusting expression variance for zero-centered normalisation
This function adjusts the variance of the gene expression according to the zero-centered normalisation.
● Data Source:
BioConductor
● Keywords: manip
● Alias: clusterNormVar
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