In rmflight/ccPaper: work for categoryCompare paper revisions

ReAnalysis based on reviewer comments

Because we have re-worked the publication as a paper about the tool, we have decided to do a re-analysis of the original data presented in the original manuscript based on the reviewer comments, as well as include other data sets.

Muscle VS Skin Denervation

The original data consisted of muscle denervation data from GSE4411, and skin denervation data from Dr. Jeffrey Petruska.

UC VS Crohn's

From GEO there is a ulcerative colitis vs crohn's disease data set available, GSE36807. This would be a nice one to try, as there is already a publication on it.

Metabolomics VS Transcriptomics

The NCI 60 database has both metabolomics and transcriptomics data available. Unfortunately, there is no control data set.

Metabolomics File:

• File Format: SAMPLENAME, TITLE, PANELNBR, CELLNBR, pname, cellname, VALUE

Ideas for analysis: slow vs fast growing, sensitive to compound vs insensitive to compound

Transcriptomics File:

• File Format: MOLTID (NCI pattern #), ACC, Gene, TITLE, MOLTNBR (NCI exp. id #), PANELNBR, CELLNBR, pname, cellname, CHIP, FEATURE_ID, UniGene, GeneID, VALUE Gene assignments are based on Unigene Build #U225 (August 2010)

rmflight/ccPaper documentation built on May 27, 2019, 9:31 a.m.