Question: Running stattest differential expression with Ballgown covariates without replicates ?
0
gravatar for baskar.aimstar2006
3.0 years ago by
baskar.aimstar20060 wrote:

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. ?

rna-seq • 2.5k views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by baskar.aimstar20060

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.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by WouterDeCoster43k

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

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by baskar.aimstar20060

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

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by baskar.aimstar20060

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

ADD REPLYlink written 3.0 years ago by genomax84k

There is a proper conclusion in that post.

There must be at least two replicates per group.

ADD REPLYlink written 3.0 years ago by WouterDeCoster43k

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

There must be at least two replicates per group.

ADD REPLYlink written 3.0 years ago by WouterDeCoster43k

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

ADD REPLYlink written 3.0 years ago by baskar.aimstar20060

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.

ADD REPLYlink written 3.0 years ago by WouterDeCoster43k

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

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by baskar.aimstar20060
0
gravatar for WouterDeCoster
3.0 years ago by
Belgium
WouterDeCoster43k wrote:

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.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by WouterDeCoster43k
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