Question

DEseq normalization paired t-test

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ningchaobj • 0

@ningchaobj-7135

Last seen 10.2 years ago

Australia

Whther can I use the normalization function to normalize my raw read counts and the perform the paired t-test to find the differicential expression genes? As we know paired t-test demands normal distribution.

deseq • 2.8k views

ADD COMMENT • link updated 10.2 years ago by Michael Love 43k • written 10.2 years ago by ningchaobj • 0

score 1 · Answer 1 · 2014-12-08

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Michael Love 43k

@mikelove

Last seen 2 days ago

United States

hi,

We recommend you to use the DESeq() function in DESeq2, as this is likely more powerful than a paired t-test. To account for the pairs you should use a design of the form: ~ individual + condition

See also this recent thread discussing this question:

RNA-seq differentially expressed gene finding methods

ADD COMMENT • link 10.2 years ago Michael Love 43k

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I want to know that if I have to perform paired t-test.I normorlize my raw counts by this way rather than rpkm values.Is it suitable?

ADD REPLY • link 10.2 years ago ningchaobj • 0

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Can you explain why you have to perform paired t-tests?

ADD REPLY • link 10.2 years ago Michael Love 43k

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You don't need to use a paired t-test to account for matching of sample sources. It is done when you include a factor for the sample source in the linear model.

ADD REPLY • link 10.2 years ago Dario Strbenac ★ 1.5k