I'm using ballgown package on the stringtie output for differential expression analysis. The .csv file like below:
ids group time rep 1 sample1 control 0 a 2 sample10 drug 24 d 3 sample11 drug 24 d 4 sample2 control 0 a 5 sample3 drug 2 b 6 sample4 drug 2 b 7 sample5 drug 2 b 8 sample6 drug 12 c 9 sample7 drug 12 c 10 sample8 drug 12 c 11 sample9 drug 24 d
I want to find DE genes between control and each time point and between various time points after using drug (eg, 2 and 12, 2 and 24, 12 and 24, 2 and 24). I used the below command for it
test = stattest(bg, feature='transcript', meas='FPKM', covariate='time', timecourse=FALSE, adjustvars='group', getFC=TRUE)
But the following error appeared:
Error in solve.default(t(mod) %*% mod) : system is computationally singular: reciprocal condition number = 2.19379e-27 In addition: Warning message: In stattest(bg, feature = "transcript", meas = "FPKM", covariate = "time", : fold changes only available for 2-group comparisons
To solve the problem, I try to filter FPKM less than 1 or even 10, but the error about "system is computationally singular" is still exist. Could you please help me out to solve this error and also the other errors about "Error in solve.default(t(mod) %*% mod)" and "fold changes only available for 2-group comparisons"?