Question: Ballgown for more than 2 group comaprison
gravatar for amy16
8 months ago by
amy160 wrote:


I would like to do three group comparison using Ballgown... When I do, I get the following warning message. I am not sure if it had calculated the differential expression based on the three groups, because this is just a warning message. If not, can you please suggest me on what code I should be using under the given circumstance?

Many thanks!!!!

> result_gene01_prr22=stattest(bgfilt_t22, feature="gene", covariate="genotype", getFC=TRUE, meas="FPKM")
Warning message:
In stattest(bgfilt_t22, feature = "gene", covariate = "genotype",  :  fold changes only available for 2-group comparisons
ids treatment genotype  
B1C1 control resistant  
B1C2 control resistant  
B1C3 control resistant  
B2C1 control susceptible
B2C2 control susceptible
B2C3 control susceptible
B3C1 control resistant  
B3C2 control resistant  
B3C3 control resistant  
B4C1 control moderately resistant
B4C2 control moderately resistant
B4C3 control moderately resistant
ADD COMMENTlink written 8 months ago by amy160
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