readTargets: read the target file
In AgiMicroRna: Processing and Differential Expression Analysis of Agilent microRNA chips

Description Usage Arguments Details Value Author(s) References See Also

The target file is a txt file created by the user where every input file (array, sample) is attached to a experimental condition

1	readTargets(infile,verbose=FALSE)

`infile`	name of the target file, for instance 'targets.micro.txt'
`verbose`	logical, if `TRUE` prints out output

In the 'target' file (see Table 1 in vignette) we specify the experimental conditions under which the data have been generated. The target file MUST contain the following mandatory columns: -FileName : Name of the array data file -Treatment : Treatment effect -GErep : Treatment effect in numeric code, from '1' to 'n', being 'n' the number of the levels of the treatment effect

Other explanatory variables specifying the experimental conditions might be also included.

A 'data.frame' containing by the columns specified in the input file targets.txt. This 'targets.txt' file must be created by the user.

Pedro Lopez-Romero

Smyth, G. K. (2005). Limma: linear models for microarray data. In: 'Bioinformatics and Computational Biology Solutions using R and Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, pages 397–420.

An example of a target file can be found in targets.micro

AgiMicroRna documentation built on Nov. 8, 2020, 5:25 p.m.