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Batch Correction
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3
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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 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
p.joshi
▴ 40
0
votes
1
reply
981
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 4.4 years ago by
Kevin Blighe
★ 3.9k • written 4.4 years ago by
lucasmiranda42
• 0
5
votes
3
replies
616
views
batch correction in DESeq2 > matrix not full rank > mitigate
DESeq2
batch correction
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
MT
▴ 10
0
votes
3
replies
948
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 4.8 years ago by
Rory Stark
★ 5.2k • written 4.8 years ago by
rm1238
• 0
1
vote
1
reply
999
views
All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2
differential expression
batch correction
design
updated 4.9 years ago by
Michael Love
42k • written 4.9 years ago by
wunderl
▴ 40
4
votes
4
replies
1.3k
views
Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2
differential expression
batch correction
updated 4.9 years ago by
Michael Love
42k • written 4.9 years ago by
wunderl
▴ 40
4
votes
5
replies
1.8k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 5.1 years ago by
Vladimir Kiselev
▴ 150 • written 5.1 years ago by
hamza_karakurt
▴ 50
7 results • Page
1 of 1
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Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results
by
swbarnes2
★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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