Question

Getting differentially expressed genes for time points

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AZ ▴ 30

@fereshteh-15803

Last seen 20 months ago

United Kingdom

Hi

I have 5 samples (from 4 patients) in bulk RNA-seq, from cancer survivors and controls

For a cancer survivor, we have two samples from month 0 and month 6

This is the experimental design

enter image description here

For getting differentially expressed genes between cancer survivors and controls, I guess I know what to do, but, for getting differential expressed genes between time point 1 and 2 of CS001 I don't know what should I do

Any help please?

edgeR DifferentialExpression limma • 1.6k views

ADD COMMENT • link updated 3.8 years ago by Gordon Smyth 52k • written 3.8 years ago by AZ ▴ 30

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Cross-posted to https://www.biostars.org/p/492071/

ADD REPLY • link 3.8 years ago Gordon Smyth 52k

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I might help somewhat if you told us at what time points the CS002, HC002 and HC003 samples were observed. Month 0? Month 6? something else? Do you have any two samples from the same Time point? In other words, do you have any biological replicates at all?

ADD REPLY • link 3.8 years ago Gordon Smyth 52k

score 3 · Answer 1 · 2021-02-19

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Gordon Smyth 52k

@gordon-smyth

Last seen 4 hours ago

WEHI, Melbourne, Australia

There isn't any statistically rigorous way to compare month 0 to month 6, because there is only one paired case, i.e. there is no replication.

ADD COMMENT • link 3.8 years ago Gordon Smyth 52k

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Sorry what if I have two technical replicates for each of these ? I mean 2 rounds of sequencing to give greater read depth)

hank you for any help

like

Samples                       condition
CS001_time point 1_1             cancer
CS001_time point 1_2             cancer
CS001_time point 2_1             cancer
CS001_time point 2_2            cancer
HC002_1                        control
HC002_2                       control
HC003_1                       control
HC003_2                       control

ADD REPLY • link 3.8 years ago AZ ▴ 30

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Makes no difference. Extra sequencing is not a replicate.

ADD REPLY • link 3.8 years ago Gordon Smyth 52k

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Sorry does it make any sense to first compare CS001_t1 and CS002 versus HC002 and HC003

then CS001_t2 and CS002 versus HC002 and HC003

and then take uncommon differentially expressed genes as related to time points?

I mean comparing time point 1 plus to another cancer sample versus two controls in one go

and comparing time point 2 plus to another cancer sample versus two controls in next go

And finally comparing the results

ADD REPLY • link 3.8 years ago AZ ▴ 30