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Batch Correction
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3
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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 4.5 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
★ 3.9k • written 4.6 years ago by
lucasmiranda42
• 0
5
votes
3
replies
645
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
986
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 5.1 years ago by
Michael Love
42k • written 5.1 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 5.1 years ago by
Michael Love
42k • written 5.1 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 5.3 years ago by
Vladimir Kiselev
▴ 150 • written 5.3 years ago by
hamza_karakurt
▴ 60
7 results • Page
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Replies
Comment: limma comparison for small sample size and how to get covariance matrix
by
Gordon Smyth
51k
Your MDS plot is better than before, but you are still not following the recommendation for making for making such plots given in the limma…
Comment: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
Also, ``` > result <- mapUniProt( from = "EMBL-GenBank-DDBJ_CDS", to = "UniProtKB", query = c("ACF95883.1") ) > result From…
Comment: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
Ugh, here's the link https://www.uniprot.org/id-mapping/uniprotkb/dd08aa16774d98ef087dc3bd708582012bba49e2/overview?fields=accession%2Cre…
Answer: Mapping Between GenBank ID's and Uniprot
by
James W. MacDonald
66k
The input should be 'EMBL-GenBank-DDBJ_CDS", as that is a GenBank ID.
Answer: XCMS2 of orbitrap data
by
Elodie
• 0
Hi, I have the same question, I have acquired MS2 data with PRM analysis and inclusion lists of several ions. I have a list of product ion…
Votes
Answer: EPIC array hg38 annotation?
Answer: Why does DESeq2 give negative log2 fold change in treatment vs control for some
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
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