Running stattest differential expression with Ballgown covariates without replicates ?

Question

[baskar.aimstar2006]

Trying ballgown stattest with covariates = group for my dataset throws me error. Can please solve based on the details below.

Error:

Error in stattest(bg, feature = "transcript", meas = "FPKM", getFC = TRUE,  covariate="group") :
  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.

Following is the dataset:

ids,group
var1,control
var2,sample1
var3,sample2
var4,sample3
var5,sample4
var6,sample5
var7,sample6
var8,sample7
var9,sample8
var10,sample9
var10,sample10
var11,sample11

Can anyone tell me how to design the model for this. ?

[WouterDeCoster]

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar.

[baskar.aimstar2006]

Thank you for your guide.... Looking for support on my question.

[baskar.aimstar2006]

I also referred to previous post related to the same question, but there is no proper conclusion.

post: Error encountered while running stattest from ballgown package

[GenoMax]

If you need to add this information edit your original post and add there.

[WouterDeCoster]

There is a proper conclusion in that post.

There must be at least two replicates per group.

[WouterDeCoster]

So you don't have biological replicates? The 11 samples are all different?

There must be at least two replicates per group.

[baskar.aimstar2006]

Current experiment model is for checking differential expression between control and each samples. What will the appropriate measure in ballgown ?

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

[baskar.aimstar2006]

Yes. That's really optimal way. i can manage to do further.

Answer 1

[WouterDeCoster]

Let me write this once more:

You need to have at least two replicates per group. That's what the error says, and it's really really required to do proper statistics. It's even often considered not enough.