Hi seniors! First of all, I am very thankful to you for being here.!
I am using a ballgown for the DEG analysis. I have two samples (b73,f1). I have no replicate. Both samples are different from each other. I wanted to do a stattest and used this command;
Command; results_transcripts <- stattest(bg_filt, feature="transcript", covariate="sex", adjustvars = c("population"), getFC=TRUE, meas="FPKM")
Error in stattest(bg_filt, feature = "transcript", covariate = "sex", :
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.
So, I thought maybe I have not enough samples to run Ballgown for the Statest. I just copied the samples and created two new samples which mean, Now I have 4 samples. And I run the same command as shown in above. Now, I got this error:
output: Coefficients not estimable: libadjust
Error in solve.default(t(mod) %*% mod) :
system is computationally singular: reciprocal condition number = 1.06159e-26
In addition: Warning message:
Partial NA coefficients for 19766 probe(s)
Request: I am new in this field and really want to learn. Could you please help me? Anyone?