Entering edit mode
2.5 years ago
biology_inform
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50
Hi all, How can I compare different transcriptomics of different RNA-Seq data results? Each study is unique and comparing LogFC values directly doesn't seem quite right to me. Is there a tool for compare them or does anyone recommend me a way to compare them ?
https://pubmed.ncbi.nlm.nih.gov/28479595/
Hi. First of all, do you have the same species or not? In case you don't, I guess you should start with defining your single-copy orthologues, generate a gene expression matrix for those genes, normalize your data (there is a new method called SCBN) and then do your differential expression. I am quite new in this field so still learning how to do this in practice In case you resolved your problem or still working on it I would love to share pipelines and knowledge in general. :)
Thanks for your response and sorry for late response :) I am still trying to find an answer to this issue. Also they are the same species. My setup is actually quite simple I have gathered different lung cancer RNA-Seq data from GEO database and I want to compare them but not manually. I want it to be in more logical. If you have any suggestions I want to to learn and apply them immediately :)
this is a very well-studied issue. Id start by going to the vignette page for a package like
DESeq2.yes, DESeq or EdgeR are common tools. just, I am not sure if different experiments can be compared in this way, I guess you should do some kind of normalization, right? Are the sequencing depth even the same in different experiments from which you took the RNAseq data? Just be sure to check those. good luck!
right, the vignette will make that clear for you if you read through it, in particular if studied alongside the manuscript for either article as well as the documentation.