readcufflinks shows error in R cummeRbund Package

Question

[Mask]

There are two samples and I have performed the analysis as given in paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334321/ . But when I performed cummeRbund it gave following output.

cuffl <-readCufflinks('diff_out')

cuffl

CuffSet instance with:

 0 samples
 0 genes
 0 isoforms
 0 TSS
 0 CDS
 0 promoters
 0 splicing
 0 relCDS

The file is attached diff_out

[Satyajeet Khare]

Are you in the working directory (cuffdiff out folder)? Can you try following?

setwd("/your_cuffdiff_out_directory_location")
cuffl <-readCufflinks()

[Mask]

Yes. In working directory only. I have attached the file (diff_out) . The size of the folder is very less. Can you download and perform cummeRbund on that

[WouterDeCoster]

I'm not sure why this thread was deleted after it was answered... reopened.

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

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Answer 1

[Satyajeet Khare]

I removed files that were not generated by cuffdiff and got this result...

CuffSet instance with:
     2 samples
     1558 genes
     1947 isoforms
     1658 TSS
     0 CDS
     1558 promoters
     1658 splicing
     0 relCDS

So my suggestion is, dont alter cuffdiff output :)

[Mask]

Can you tell me which all files did you remove from the folder? Thank you

[Satyajeet Khare]

You will get more help from the community if you up-vote answers to your questions than your own questions and comments.

[Mask]

okay... Can you tell me which all files did you remove from the folder?

[GouthamAtla]

Can someone do that ? up-vote own posts ?

[Satyajeet Khare]

Looks like you cannot. My bad. Just saw score rising from 0 to 200 in a matter of minutes so grew suspicious. Apologies.

[GouthamAtla]

It looks suspicious though, 0 to 200, which I had noticed as well.

[Ram]

It is definitely suspicious. A warning has been issued to @Mask. I will also keep an eye out for future infarctions.

[Ram]

Upvote baiting is not good etiquette.