Question: What to write in the y axis of RNA-Seq plot
0
gravatar for mfc
3.9 years ago by
mfc0
Germany
mfc0 wrote:

Hello everybody!

I am new to the guidelines of RNA-Seq data and I would like to know what do people normally write in the y axis of the plots in papers. 

We want to show a comparison of RNA-Seq with qPCR data. For the qPCR we have normalised gene expression data (log2) that was previously normalised to an internal control and to reference genes. For the RNA-Seq we just have FPKM. Is it correct to write Normalised Gene Expression (FPKM)? 

 

Thanks!

pcr rna-seq fpkm guidelines • 1.8k views
ADD COMMENTlink modified 3.9 years ago by Biostar ♦♦ 20 • written 3.9 years ago by mfc0
3

You are overthinking it. If what you show for RNA-Seq is the FPKM count, write that. You should always adhere to the KISS principle when creating and labeling plots.

ADD REPLYlink written 3.9 years ago by David Westergaard1.4k

Thanks! I didnt know about the KISS principle ;)

ADD REPLYlink written 3.9 years ago by mfc0
Keep it short and simple is different between bioinformaticans and Biologists. A bioinformaticIan would want log2(counts per million), a biologist wants Expression by RNAseq
ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by Irsan6.9k
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