Question

Represent expression values

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9.8 years ago

int11ap1 ▴ 470

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 • 3.3k views

ADD COMMENT • link updated 2.4 years ago by Ram 43k • written 9.8 years ago by int11ap1 ▴ 470

Ram · Answer 1 · 2014-07-14

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9.8 years ago

aditi.qamra ▴ 270

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 2here. This should be a good start if you are just looking to understand the terms in general.

ADD COMMENT • link updated 2.4 years ago by Ram 43k • written 9.8 years ago by aditi.qamra ▴ 270

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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 REPLY • link 9.8 years ago by int11ap1 ▴ 470

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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 REPLY • link updated 2.4 years ago by Ram 43k • written 9.7 years ago by aditi.qamra ▴ 270