plgem.write.summary {plgem} | R Documentation |
This function writes the list of differentially expressed genes/proteins
obtained via a call to either plgem.deg
or
run.plgem
to a series of files in the current working directory.
plgem.write.summary(x, verbose=FALSE)
x |
list ; the output of either plgem.deg or
run.plgem , i.e. a list of list(s) of named vectors. |
verbose |
logical ; if TRUE , comments are printed out while
running. |
The gene or protein lists are written to the current working directory, using conveniently chosen filenames that reflect the specific comparisons that were performed (i.e. which experimental condition was compared to the baseline) and the specific significance threshold that were used in the DEG selection step.
The function returns no value. It is called for its side effect to write files to the working directory.
Mattia Pelizzola mattia.pelizzola@gmail.com Norman Pavelka nxp@stowers-institute.org
Pavelka N, Pelizzola M, Vizzardelli C, Capozzoli M, Splendiani A, Granucci F, Ricciardi-Castagnoli P. A power law global error model for the identification of differentially expressed genes in microarray data. BMC Bioinformatics. 2004 Dec 17;5:203.; http://www.biomedcentral.com/1471-2105/5/203
Pavelka N, Fournier ML, Swanson SK, Pelizzola M, Ricciardi-Castagnoli P, Florens L, Washburn MP. Statistical similarities between transcriptomics and quantitative shotgun proteomics data. Mol Cell Proteomics. 2007 Nov 19; http://www.mcponline.org/cgi/content/abstract/M700240-MCP200v1
## Not run: data(LPSeset) LPSdegList <- run.plgem(LPSeset) plgem.write.summary(LPSdegList, verbose=TRUE) ## End(Not run)