## User: Giard

Giard •

**10**- Reputation:
**10**- Status:
- New User
- Location:
- france
- Last seen:
- 2 years, 8 months ago
- Joined:
- 2 years, 10 months ago
- Email:
- b*******@gmail.com

#### Posts by Giard

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... Can you try this! Change this line:
terms <- stack(lapply(mget(cats, GO:0005615, ifnotfound=NA), extracellular space))
To this:
terms <- stack(lapply(mget(cats, "GO:0005615", ifnotfound=NA), extracellular space))
...

written 2.7 years ago by
Giard •

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Comment:
C: how DESeq calculates p-value ?

... Thanks for that. Time to start my journey toward limma and DESeq-2.
...

written 2.8 years ago by
Giard •

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Comment:
C: how DESeq calculates p-value ?

... Thanks. I would definitely follow your suggested topics. But I'd like to take the chance and asking a couple of more questions related, please:
1- You mentioned that estimated Mean and Variance are not used to calculate p-value, then why are they estimated in the first place if they are not plugge ...

written 2.8 years ago by
Giard •

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Comment:
C: how DESeq calculates p-value ?

... Thanks for your recommendation and information.
...

written 2.8 years ago by
Giard •

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Comment:
C: how DESeq calculates p-value ?

... Thanks Simon, I don't have a right to be upset as I am one of those looking for help NOT bossing around :)
As I am new into this and watched some tutorials as well as starting with DESeq-1, that is why I am so willing to understand it first then go to DESeq-2.
To state it again, in addition to th ...

written 2.8 years ago by
Giard •

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Comment:
C: how DESeq calculates p-value ?

... I really don't get it. thousands of researchers using and asking about expression analysis and DESeq while no one can give a proper explanation on basic questions.
@ at least thanks for those above who tried to say some.
...

written 2.8 years ago by
Giard •

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Comment:
C: how DESeq calculates p-value ?

... I wonder if DESeq2 changed p-value computation compared to DESeq?
If it is changed, how DESeq2 does it then? Because after all we will be used the latest which is DESeq2.
...

written 2.8 years ago by
Giard •

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... Hi everyone,
I am in a basic level of statistics and using DESeq package for RNA-seq. I don't understand how DESeq calculates p-value exactly. If we simplify statistics, for two sample mean comparison we either use z-test or t-test, right?
How about in DESeq?
In DESeq paper :
...

written 2.8 years ago by
Giard •

**10**• updated 2.8 years ago by Ryan C. Thompson ♦**7.0k**#### Latest awards to Giard

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