Error Analysis for 1D Electrophoresis Gels

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Description

This function analyzes fingerprint replicate data. Replicates are repeated measurements of the same sample in one or more gels, which allows the reproducibility of the measurement to be ascertained.

Usage

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call_erra(rep.file, work_dir = ".", dnum = 1, sd = 4, delete = FALSE)

Arguments

rep.file

is the full name and path of the replicate file

work_dir

is where the datasets should be stored

dnum

is the file number

sd

is the standard deviation needed to calculate all things, Salamon et al. (1998) suggested a value of 4 for sd

delete

logical value indicating if you want to delete any pre-existing acm.par files. Default is FALSE

Value

the parameter filed called acm.par, needed by call_acm. This file contains information on about the measurement error present in the data.

Note

call_erra doesn't work for unequal number of trials. This function needs to be run before call_acm.

Author(s)

Andrea Benedetti andrea.benedetti@mcgill.ca

Sahir Rai Bhatnagar

XiaoFei Zhao

References

Salamon et al. (1998) Accommodating Error Analysis in Comparison and Clustering of Molecular Fingerprints. Emerging Infectious Diseases Vol. 4, No. 2, April-June 1998

Abasci LLC. JAMES v1.0 User Documentation. 2002.

Examples

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#generate the error parameter file needed by call_acm
call_erra("replicates.in",  dnum=1, sd=1, delete=TRUE)