Question: question on GSEAlm
0
10.8 years ago by
Mark W Kimpel830
Mark W Kimpel830 wrote:
I've been successfully using GSEAlm for purposes quite similar to the examples in the vignette without difficulty. Now I would like to apply this package to a list of summary statistics derived from a one-sample t-test of 6 Cohen's D measurements. My options would seem to be either modeling the CD measurements, a one factor, one level, design; or, just using the computed t.statistics. R's basic function of lm doesn't seem to like one-sample tests (understandably, see my example below) yet I can't figure out how to do GSEA using just a pre-computed list of stats. > a <- c(-1, 1, 0, 100, 3) > fac <- factor(rep("A", 5)) > lm(a ~ fac) Error in contrasts<-(*tmp*, value = "contr.treatment") : contrasts can be applied only to factors with 2 or more levels ------------------------------------------------------------ Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** [[alternative HTML version deleted]]
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