Hi all,
Please let me know how I should go about in fixing this error.
> pData(bg) ids treatment genotype 1 B1C_01 control resistant 2 B1T_01 inoculated resistant > prr01_trans_result=stattest(bg_filt, feature="transcript", covariate="treatment", getFC=TRUE, meas="FPKM") Error in stattest(bg_filt, feature = "transcript", covariate = "treatment", : There must be at least two replicates per group. Make sure covariate is categorical; if continuous, consider the timecourse option, or specify your own models with mod and mod0.
PS: I do not have replicates for this experiment.
Thanks
Thanks Alyssa for the reply and the good news that I can rank the genes/transcripts by fold change. Is this fold change calculation script described in the Ballgown manual? Can u please direct me on how I go about it?
PS: I understand and I totally agree with you that without replicates, one can not perform statistical inference, so can't calculate p-values, confidence intervals, standard errors or anything like that. (Variance is undefined when you have only one item).
Thanks
Amy
Please see https://github.com/alyssafrazee/ballgown#accessing-assembly-data for information on how to access the fold change information for each transcript (or gene or exon) for each sample.
You will then need to write your own R code to calculate the expression fold change between the two samples for each transcript.
Good luck!
Thanks for the reply...