Question: Error about using cummeRbund package to load cuffdiff output data
gravatar for 673422688
19 months ago by
6734226880 wrote:

I had analyzed the RNA-seq data with Tophat-Cufflinks-Cuffdiff procedure. when I used the cummeRbund package by R I can not read the diffout data correctly from the Cuffdiff and showed Error: Faceting variables must have at least one value, After input Cuff,R showed: CuffSet instance with: 2 samples 47632 genes 0 isoforms 0 TSS 0 CDS 0 promoters 0 splicing 0 What is the reason for relCDS?   Here is my code: Setwd("D:/RNA-seq data/B6_SMX") ##RNA-seq Cuffdiff diffout path Library(cummeRbund) Cuff <- readCufflinks() dispersionPlot(genes(cuff))

Thank you so much for answering my question.

rna-seq cummerbund R • 399 views
ADD COMMENTlink written 19 months ago by 6734226880

that "pipeline" is deprecated for years now, perhaps consider to switching to something more recent/modern ? Hisat2-stringtie-ballgown for instance

ADD REPLYlink written 19 months ago by lieven.sterck9.0k

I know it. Since I am a beginner, my teacher wants me to run the tophat-cufflinks-cuffdiff pipeline firstly and independently to undersatand some basic knowledge about linux and transcriptome. If you have some solutions,many thanks.

ADD REPLYlink written 19 months ago by 6734226880

mmyeah ... still you will/can get the some insights using the more up-to-date version ;)

ADD REPLYlink written 19 months ago by lieven.sterck9.0k
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