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Batch Correction
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3
votes
3
replies
1.7k
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fastMNN based correction for large multi-run experiment requires a similar population set in all the individual datasets?
scrna-seq
integration
batch correction
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
p.joshi
▴ 40
0
votes
1
reply
1.1k
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 4.6 years ago by
Kevin Blighe
★ 4.0k • written 4.6 years ago by
lucasmiranda42
• 0
5
votes
3
replies
672
views
batch correction in DESeq2 > matrix not full rank > mitigate
DESeq2
batch correction
updated 4.7 years ago by
James W. MacDonald
66k • written 4.7 years ago by
MT
▴ 10
0
votes
3
replies
1.0k
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 5.0 years ago by
Rory Stark
★ 5.2k • written 5.0 years ago by
rm1238
• 0
1
vote
1
reply
1.0k
views
All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2
differential expression
batch correction
design
updated 5.1 years ago by
Michael Love
42k • written 5.1 years ago by
wunderl
▴ 40
4
votes
4
replies
1.5k
views
Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2
differential expression
batch correction
updated 5.1 years ago by
Michael Love
42k • written 5.1 years ago by
wunderl
▴ 40
4
votes
5
replies
1.9k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 5.3 years ago by
Vladimir Kiselev
▴ 150 • written 5.3 years ago by
hamza_karakurt
▴ 60
7 results • Page
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Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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Lluís Revilla Sancho
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to
maltethodberg
▴ 180
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Michael Love
42k
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★ 1.1k
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