User: wunderl

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wunderl20
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Posts by wunderl

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (R
... 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 wunderl20
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Answer: A: DESeq2 GLM modelling and Wald's test
... 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 wunderl20
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Comment: C: Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (R
... 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 wunderl20
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All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
... 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 ...
deseq2 differential expression design batch correction written 5 weeks ago by wunderl20 • updated 4 weeks ago by Michael Love24k
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
... 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 ...
deseq2 differential expression batch correction written 5 weeks ago by wunderl20 • updated 5 weeks ago by Michael Love24k
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featureCounts Does Not Correctly Parse File Names
... 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/ ...
rsubread featurecounts written 9 weeks ago by wunderl20 • updated 9 weeks ago by Gordon Smyth38k

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