limma (version 3.28.6)

write.fit: Write MArrayLM Object to a File

Description

Write a microarray linear model fit to a file.

Usage

write.fit(fit, results=NULL, file, digits=3, adjust="none", method="separate",
          F.adjust="none", sep="\t", ...)

Arguments

fit

object of class MArrayLM containing the results of a linear model fit

results

object of class TestResults

file

character string giving name of file

digits

integer indicating precision to be used

adjust

character string specifying multiple-testing adjustment method for the t-statistic P-values, e.g., "BH". See p.adjust for the available options. If NULL or "none" then the P-values are not adjusted.

method

character string, should the P-value adjustment be "global" or "separate" for each contrast.

F.adjust

character string specifying adjustment method for the F-statistic P-values.

sep

the field separator string. Values in the output file will be separated by this string.

...

other arguments are passed to write.table

Value

• No value is produced but a file is written to the current working directory.

Details

This function writes a tab-delimited text file containing for each gene (1) the average log-intensity, (2) the log-ratios, (3) moderated t-statistics, (4) t-statistic P-values, (5) F-statistic if available, (6) F-statistic P-values if available, (7) classification if available and (8) gene names and annotation.

See Also

write in the base library. An overview of linear model functions in limma is given by 06.LinearModels.