Showing : batch effect • reset
7
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3
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3.8k
views
SVA: Including variable of interest in ComBat model matrix
combat sva SVA sva ComBat batch effect
updated 9.4 years ago by ▴ 870 • written 9.4 years ago by ▴ 20
6
votes
6
replies
6.2k
views
Questions regarding SVA batch effect normalizazion into DeSeq2 workflow
sva deseq2 batch effect
updated 9.4 years ago by 43k • written 9.4 years ago by • 0
3
votes
8
replies
3.7k
views
Batch effects in limma
limma batch effect
updated 9.4 years ago by ★ 29k • written 9.4 years ago by • 0
4
votes
12
replies
5.9k
views
remove batch effect using limma
limma rnaseq batch effect pearsoncorrelation
updated 9.6 years ago by ★ 29k • written 9.6 years ago by • 0
4
votes
3
replies
1.4k
views
EdgeR: is more than one control per batch an issue?
edgeR batch effect
updated 9.6 years ago by ★ 29k • written 9.6 years ago by ▴ 80
1
vote
2
replies
2.4k
views
Evaluation of diagnostic plot resulted from ComBat function regarding batch effect correction of a merged microarray dataset
ComBat diagnostic plot batch effect affymetrix microarrays sva
updated 9.6 years ago by ▴ 870 • written 9.6 years ago by ▴ 840
1
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2
replies
1.8k
views
Batch effect correction for ANOVA-like DE analysis in edgeR
edgeR batch effect
9.6 years ago Manoj Hariharan ▴ 110
2
votes
2
replies
2.9k
views
order of covariates for GLM with edgeR
edger differential expression covariate batch effect glm
updated 9.7 years ago by 53k • written 9.7 years ago by ▴ 90
8
votes
14
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3.6k
views
Batch with only one sample or condition
limma batch effect
updated 9.8 years ago by 53k • written 9.8 years ago by ▴ 70
0
votes
1
reply
2.1k
views
SomaticSignatures: negative entries after ComBat adjustment
sva somaticsignatures batch effect nmf
updated 9.8 years ago by ▴ 650 • written 9.8 years ago by • 0
0
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0
replies
1.5k
views
NOISeq error message while using ARSyNseq batch correction function
noiseq batch effect ARSyNseq
9.9 years ago lina.faller ▴ 10
2
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1
reply
2.3k
views
differential expressed genes, paired samples and multiple factors
edgeR batch effect differential gene expression paired samples
updated 9.9 years ago by ★ 29k • written 9.9 years ago by ▴ 10
10
votes
6
replies
12k
views
Estimating and removing batch effects from rna-seq dataset
sva batch effect rnaseq removebatcheffect() limma
updated 9.9 years ago by ▴ 650 • written 9.9 years ago by ▴ 110
1
vote
1
reply
6.1k
views
Combat generating negative values, should I log2 transform first?
combat batch effect
updated 9.9 years ago by ▴ 870 • written 9.9 years ago by ▴ 60
20
votes
18
replies
6.2k
views
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
limma batch effect ComBat differential gene expression
updated 9.9 years ago by ▴ 870 • written 10.0 years ago by ▴ 840
7
votes
7
replies
11k
views
batch effect : comBat or blocking in limma ?
batch effect combat limma block
updated 10.0 years ago by ★ 7.9k • written 10.0 years ago by ▴ 70
4
votes
7
replies
4.6k
views
removeBatchEffect -- warnings and results
batch effect edgeR
10.0 years ago pavlidisp ▴ 10
1
vote
1
reply
3.0k
views
sva and svaseq for unsupervised analysis of expression data
sva combat gene expression batch effect rnaseq
updated 10.0 years ago by ▴ 650 • written 10.0 years ago by ▴ 10
0
votes
2
replies
1.8k
views
Considering both : batch effect and patient to patient variation in EdgeR analysis
EdgeR batch effect patient rnaseq
10.0 years ago n.deshpande • 0
0
votes
3
replies
2.4k
views
Query about DEXSeq
dexseq batch effect PCA
10.0 years ago n.deshpande • 0
1
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2
replies
3.4k
views
Problem with n.sv in sva package
batch effect sva
10.1 years ago daih • 0
6
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5
replies
5.1k
views
voom + removeBatchEffect + gene clustering
voom limma clustering removebatcheffect() batch effect
updated 10.2 years ago by 53k • written 10.2 years ago by ▴ 10
6
votes
11
replies
6.7k
views
Limma, blocking batch effect
limma batch effect
updated 10.2 years ago by ▴ 840 • written 10.2 years ago by ▴ 20
1
vote
2
replies
1.9k
views
Question about the proper way to combine Illumina Human HT-12 v4 expression datasets from different labs
combat batch effect
10.5 years ago jaro.slamecka ▴ 140
3
votes
2
replies
11k
views
Batch effect removal in edgeR
edger batch effect
updated 10.7 years ago by 53k • written 10.7 years ago by ▴ 50
125 results • Page 3 of 3
Recent ...
Replies
Comment: DESeq2 interactions by Michael • 0
Brilliant, thank you!
Answer: readBam vs read_bam_insert_metrics by lincolnprice964 ▴ 10
Yes read_bam_insert_metrics() can take input directly from a BAM file or from an object created with readBam(). Use whichever fits best in …
Comment: DESeq2 interactions by lincolnprice964 ▴ 10
If you want HP vs CNP directly, set up the interaction model: dds <- DESeqDataSetFromTximport(genes.salmon, coldata, ~ pollution + temp + …
Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Votes
Comment: DESeq2 interactions
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
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