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.
FE2(fileName, cy0, strain)
fileName | A string representing the input file name. No default. |
---|---|
cy0 | A number representing the dye color used for the control sample
( |
strain | A string representing the output file name (the sample name, typically a yeast strain). No default. |
A flat file with four columns:
chr number
Probe start position (bp number)
Probe end position (bp number)
Log2 ratio
Load this file using base R function read.table('/path/to/file', header = TRUE)
.
# NOT RUN { FE2('GSM873122.txt', 3, 'wt_Rec8_1_Cy3') FE2('247a.txt', 3, '247a') # }