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batch correction
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3
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1.0k
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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 3.4 years ago by
Aaron Lun
★ 28k • written 3.4 years ago by
p.joshi
▴ 40
0
votes
1
reply
618
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 3.5 years ago by
Kevin Blighe
3.8k • written 3.5 years ago by
lucasmiranda42
• 0
5
votes
3
replies
402
views
batch correction in DESeq2 > matrix not full rank > mitigate
DESeq2
batch correction
updated 3.6 years ago by
James W. MacDonald
63k • written 3.6 years ago by
MT
▴ 10
0
votes
3
replies
608
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 3.8 years ago by
Rory Stark
★ 4.9k • written 3.8 years ago by
rm1238
• 0
1
vote
1
reply
692
views
All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2
differential expression
batch correction
design
updated 4.0 years ago by
Michael Love
40k • written 4.0 years ago by
wunderl
▴ 40
4
votes
4
replies
919
views
Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2
differential expression
batch correction
updated 4.0 years ago by
Michael Love
40k • written 4.0 years ago by
wunderl
▴ 40
4
votes
5
replies
1.3k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 4.2 years ago by
Vladimir Kiselev
▴ 150 • written 4.2 years ago by
hamza_karakurt
▴ 50
7 results • Page
1 of 1
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Comment: Interpret plot from DiffBind
by
Chris
• 0
I sorted Fold decreasing. When I filter out genes with fold > 2.5 and filter out genes with fold < -2.5 and got 1287 genes appear in both s…
Comment: Interpret plot from DiffBind
by
Chris
• 0
Thank you so much. I think the function is `dba.report()`. more_open_in_disease: 79113 more_closed_in_disease: 36828 So there are 79113 pea…
Comment: Interpret plot from DiffBind
by
Chris
• 0
Hi Rory, when I run your code, I got this error: Error: unexpected ')' in: " matrices_color=list(c("white", "ma…
Comment: Can DESeq2 handle huge variations in sequencing depth among samples?
by
Gopinath
• 0
Thanks for your suggestion, Michael. I will try that strategy.
Comment: Error with IsoformSwitchAnalyzer: analyzePFAM
by
Callum
• 0
It seems that the problem doesn't occur when the input file is significantly shortened to ~20 transcripts! Please help
Votes
A: ggbio error: Objects of type OrganismDb not supported by autoplot
Answer: DeSEQ 2 Error: some values in assay are negative
DESeq2 Error from Installing a Package
Answer: Using PEER to identify hidden confounders in RNA-seq data (not working)
Comment: Error: biomaRt has encountered an unexpected server error.
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