Hello all;
I have a RNA-SEQ data set that has three genotypes that were each exposed to three different treatments (2 pathogens and a control). I know the infection outcome for each of my genotypes when they are exposed to one or the other pathogen. I would like to know if the variation in gene expression is better explained by including the infection status nested within genotype. in other words, I would like to test between:
fit0<- counts~genotype
fit1<- counts~genotype%in%infection_status
However, I am unable to obtain a fit1. I get the error message (in addition to some warnings):
Error: all(na.omit(res[, "df.residual"] == df.residual)) is not TRUE
I would appreciate any help.
Seanna
I have a RNA-SEQ data set that has three genotypes that were each exposed to three different treatments (2 pathogens and a control). I know the infection outcome for each of my genotypes when they are exposed to one or the other pathogen. I would like to know if the variation in gene expression is better explained by including the infection status nested within genotype. in other words, I would like to test between:
fit0<- counts~genotype
fit1<- counts~genotype%in%infection_status
However, I am unable to obtain a fit1. I get the error message (in addition to some warnings):
Error: all(na.omit(res[, "df.residual"] == df.residual)) is not TRUE
I would appreciate any help.
Seanna
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