User: wunderl
wunderl • 20
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Posts by wunderl
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... Thank you for the elaboration. I didn't realize `removeBatchEffect` operated at the log-transformed level, I can see now why it is distinct from the suite of tools `DESeq2` provides. The point about GC bias was very interesting as well. I am very new to this sort of space so I really appreciate th ...
written 5 weeks ago by
wunderl • 20
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... I am new to `DESeq2` myself so take this answer with a grain of salt.
I was initially confused by the difference between a `Wald test` and a `t-test` as well. To explain why a Wald test is used we first need to explain why we are fitting a generalized linear model (`GLM`).
A **lot** is going on ...
written 5 weeks ago by
wunderl • 20
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... Thanks Michael, I really appreciate the help!!
I will look into Salmon. So far my pipeline has been `STAR` --> `featureCounts` --> `DESeq2`. Would you say that not correcting for GC bias is a significant oversight?
Also, is there a reason `DESeq2` does not have anything analogous to `limma ...
written 5 weeks ago by
wunderl • 20
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... I have the following design matrix:
```
batch treatment
A 1
A 2
A 3
B 1
B 2
B 3
C 1
C 2
C 3
> batch
[1] A A A B B B C C C
Levels: A B C
> treatment
[1] 1 2 3 1 2 3 1 2 3
Levels: 1 2 3
```
I wo ...
written 5 weeks ago by
wunderl • 20
• updated
4 weeks ago by
Michael Love ♦ 24k
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... I am analyzing bulk RNA data from neurons derived from iPSC cells. The experimental design matrix is as follows:
| Lineage | | Method
------------- | ------------
A | |1
A | | 2
A | | 3
B | | 1
B | | 2
B | | 3
C | | 1
C | | 2
C | | 3
Here `lineage` indicates what iPSC line the neuronal ...
written 5 weeks ago by
wunderl • 20
• updated
5 weeks ago by
Michael Love ♦ 24k
1
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... When using Rsubread v 1.28.1 it sucessfully parsed my input file names by removing the file path and just keeping the names. As of the current version, however, the names contain the entire file path, this makes for very long and ugly column names.
Example
----
Setup
---
files: /path/to/file/here/ ...
written 9 weeks ago by
wunderl • 20
• updated
9 weeks ago by
Gordon Smyth ♦ 38k
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