Question: Error about using cummeRbund package to load cuffdiff output data
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gravatar for 673422688
7 months ago by
6734226880
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 • 219 views
ADD COMMENTlink written 7 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 7 months ago by lieven.sterck6.4k

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 7 months ago by 6734226880

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

ADD REPLYlink written 7 months ago by lieven.sterck6.4k
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