Question: Represent expression values
0
gravatar for int11ap1
5.4 years ago by
int11ap1380
Barcelona
int11ap1380 wrote:

Hello,

I'm dealing with RNA-seq data. I have expression values in FPKM.

Should I plot them as RPKM, or using `log2`? Why?

Thanks.

rna-seq rpkm • 2.3k views
ADD COMMENTlink modified 3.2 years ago by Biostar ♦♦ 20 • written 5.4 years ago by int11ap1380
0
gravatar for aditi.qamra
5.4 years ago by
aditi.qamra260
Toronto
aditi.qamra260 wrote:

Depends on what your end objective is. Usually fold changes are plotted as log expressions unless you wish to transform your expression value for some specific purpose.

An  article was referred in biostars Rnaseq Fpkm Quantile Normalization -  http://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/ . This should be a good start if you are just looking to understand the terms in general.

ADD COMMENTlink written 5.4 years ago by aditi.qamra260

Thanks to answer. I mean, I have two sets of genes, and I want the tests are differentially expressed by doing a t.test. However, the significance changes a lot using FPKM values and log10+1 values.

ADD REPLYlink written 5.4 years ago by int11ap1380

How did you decide upon using a t-test for differential expression determination ? I would suggest using google with search terms like ' differential expression RNAseq' and go through the wealth of information there. You can start by reading about R packages like DESeq2/EdgeR and learn what they do for this problem and why 

ADD REPLYlink written 5.4 years ago by aditi.qamra260
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