FE2: Microarray probe log2 ratios

In luisvalesilva/hwglabr: Collection of R functions used in the Hochwagen Lab

Description

This function allows you to extract Log2 ratios for all probes in a microarray. It takes as input the raw txt files found in the lab's microarray database (at 'Labshare/HTGenomics/Microarray_database/arrays') or downloaded from GEO.

Usage

FE2(fileName, cy0, strain)

Arguments

fileName	A string representing the input file name. No default.
cy0	A number representing the dye color used for the control sample (3 for cy3 or 5 for cy5). No default.
strain	A string representing the output file name (the sample name, typically a yeast strain). No default.

Value

A flat file with four columns:

1. chr number

2. Probe start position (bp number)

3. Probe end position (bp number)

4. Log2 ratio

Load this file using base R function read.table('/path/to/file', header = TRUE).

Examples

## Not run: 
FE2('GSM873122.txt', 3, 'wt_Rec8_1_Cy3')

FE2('247a.txt', 3, '247a')

## End(Not run)

luisvalesilva/hwglabr documentation built on May 21, 2019, 8:56 a.m.