Question: "fold change" question when using ballgown
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gravatar for hytxnt
4 weeks ago by
hytxnt10
hytxnt10 wrote:

hi everyone ,i am a newer to ballgown ,and i am practicing the code in 《Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown 》. but i have some question when i am trying to understand it : we have a set of data, and the covariate is "sex" inculd male and femal, after the "stattest" ,we could get the "fc" vaule ,but i am confused that dose this "fc" comes from male/female or female/male ,which exactly means when fc>1, does that means male over expressed batter than female or completely converse.

if there are some function that i dont kown which lead to this question ,please reply,thank you very much.

rna-seq • 190 views
ADD COMMENTlink modified 4 days ago by Biostar ♦♦ 20 • written 4 weeks ago by hytxnt10
1

I ask this before going into the question: Do you really want to investigate differential transcript usage rather than differential gene expression? I know the protocol you mention was published in a high impact journal and people often blindly start using it without realizing that for standard differential expression analysis on the gene level it is not the right thing to do, and there are imho better, more intuitive, computationally less expensive and especially better-documented alternatives today.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by ATpoint40k

can you suggest the document ? in the gene level ? sorry to bother you ,i dont mean that ,i just want to analyse the data,and find the wanting gene . in the begining i was suggested to pactice hisat2 and stringtie ,so i searched "that" paper out .......

ADD REPLYlink written 4 weeks ago by hytxnt10

I understand that maybe language barrier can be a bit tricky sometimes (I and many others here are not native speakers as well) but please try to be precise. No need to apologize for anything :)

i just want to analyse the data,and find the wanting gene

What does that mean? Do you want to know whether a gene is differentially-expressed or whether a transcript is differential?

For gene level analysis I suggest you follow this guide: https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

ADD REPLYlink written 4 weeks ago by ATpoint40k

i want to kown which gene is overexpressed and find the Promotor of this gene, i dont want an exact gene actually .... sorry my bad

ADD REPLYlink written 4 weeks ago by hytxnt10

I suggest you follow the linked workflow.

ADD REPLYlink written 4 weeks ago by ATpoint40k

thank you so much!!! the web lock me down because i have post too much !!! ...but ... although you suggested another protocol with fresh software , i still want to know the answer of my original question ... sorry QwQ

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by 15831492730
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