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Batch Correction
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reset
3
votes
3
replies
1.6k
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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 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
p.joshi
▴ 40
0
votes
1
reply
1.0k
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 4.5 years ago by
Kevin Blighe
★ 3.9k • written 4.5 years ago by
lucasmiranda42
• 0
5
votes
3
replies
628
views
batch correction in DESeq2 > matrix not full rank > mitigate
DESeq2
batch correction
updated 4.6 years ago by
James W. MacDonald
66k • written 4.6 years ago by
MT
▴ 10
0
votes
3
replies
976
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 4.9 years ago by
Rory Stark
★ 5.2k • written 4.9 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 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
wunderl
▴ 40
4
votes
4
replies
1.4k
views
Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2
differential expression
batch correction
updated 5.0 years ago by
Michael Love
42k • written 5.0 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 5.2 years ago by
Vladimir Kiselev
▴ 150 • written 5.2 years ago by
hamza_karakurt
▴ 60
7 results • Page
1 of 1
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Replies
Comment: Trouble reading samplesheet in with diffbind to create dba
by
Mallory
• 0
Thank you for your reply! There mustve been something wierd going on with my peak formats as you pointed out. I recalled all the peaks and …
Answer: Trouble reading samplesheet in with diffbind to create dba
by
Anthony
• 0
I was struggling with this today too. For me it happened because my peak files were not in the correct format. The "10 elements" refers to …
Comment: gds in GEOmetadb 2023-06-26 version is empty
by
Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
James W. MacDonald
66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat
by
Michael Love
42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Votes
Answer: How to do DESeq2 on Kallisto Data
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
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