Question: Please help with ballgown problem
gravatar for Sara
16 months ago by
Sara0 wrote:

Hi all,

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"? 



ADD COMMENTlink modified 16 months ago • written 16 months ago by Sara0
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