sFiltertBH {CLL} | R Documentation

## Boolean values for specific filtering based on the t-test

### Description

sFiltert is a named vector of booleans indicating whether a gene passed the specific and non-specific filtering steps. The nonspecific filtering step was described in the nsFilter man page. The specific filtering was to perform row t-tests, then perform p-value adjustment using the Benjamini & Hochberg method (using the mt.rawp2adjp function in the multtest package with the "BH" procedure), and finally include the gene if its adjusted p-value was less than 0.35. So to have a TRUE value in sFiltertBH, the gene must have an IQR greater than or equal to the median IQR and must have a BH adjusted p-value less than 0.35.

A TRUE value indicates that the gene passed the filtering step and should be included in further analysis.

### Usage

    data(sFiltert)

### Format

A named vector of logicals. The names correspond to the Affymetrix identifiers and the values are booleans indicating whether the gene passed the nonspecific and specific filtering (based on adjusted t-test p-values).

### Source

The CLL microarray data came from Dr. Sabina Chiaretti at Division of Hematology, Department of Cellular Biotechnologies and Hematology, University La Sapienza, Rome, Italy and Dr. Jerome Ritz at Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.

### Examples

    data(sFiltertBH)
    data(sCLLex)
    sCLLexSF<-sCLLex[sFiltertBH, ]

[Package CLL version 1.2.4 Index]