Showing : Batch • reset
4
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1
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1.2k
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on which data type limma::removeBatchEffect can be applyed?
batch limma
updated 15 months ago by ★ 4.0k • written 15 months ago by ▴ 50
0
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1
reply
948
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Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 20 months ago by 41k • written 20 months ago by • 0
1
vote
7
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1.3k
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Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 2.2 years ago by 65k • written 2.2 years ago by ▴ 10
0
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2
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1.0k
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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 2.3 years ago by ★ 13k • written 2.3 years ago by • 0
4
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7
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3.4k
views
DESeq2 one group vs multiple groups comparison in presence of batch effect
deseq2 comparison batch
updated 3.4 years ago by • 0 • written 4.7 years ago by • 0
0
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1
reply
934
views
Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 3.4 years ago by ★ 3.9k • written 3.4 years ago by • 0
0
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5
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1.7k
views
DeSeq2 with three batches - Remove batch Effect
deseq2 batch removebatch effect
updated 3.5 years ago by 41k • written 3.5 years ago by ▴ 40
1
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4
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1.7k
views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA zinbwave batch IntegratedData
updated 3.6 years ago by ▴ 950 • written 3.6 years ago by ★ 1.5k
2
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8
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4.2k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
3.7 years ago Pietro ▴ 40
0
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2
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677
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DESEQ2: Error in checkFullRank(modelMatrix)
deseq2 miRNASeq designmatrix Batch
updated 4.1 years ago by 41k • written 4.1 years ago by • 0
0
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3
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948
views
Highly variable gene analysis including RUVs batch correction
deseq2 RUV batch highly variable genes
updated 4.2 years ago by • 0 • written 4.2 years ago by • 0
0
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1
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1.2k
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2 ruv batch
updated 4.6 years ago by 41k • written 4.6 years ago by • 0
3
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3
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975
views
DESeq2 indirect batch effect removal
deseq2 batch
updated 4.6 years ago by 41k • written 4.6 years ago by • 0
6
votes
6
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1.6k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma paired batch
updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 20
10
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18
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16k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
4.9 years ago Mozart ▴ 30
0
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1
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766
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 5.0 years ago by 41k • written 5.0 years ago by ▴ 30
3
votes
5
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1.4k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 40
0
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3
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940
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DESEQ2 Batch effect
deseq2 batch
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
3
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3
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930
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Correcting the batch effect in Edgeseq data
DESeq2 Edgeseq batch
updated 5.3 years ago by 41k • written 5.3 years ago by ▴ 30
0
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4
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2.5k
views
DESeq2: Outliers, covariates and number of replicates
deseq2 ruvseq cookscutoff covariates batch
7.4 years ago j.viana • 0
2
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1
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1.1k
views
Does order of removeBatchEffect() and DE subsetting matter for clustered heat map visualization?
rna-seq edgeR limma removebatcheffect() batch
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 80
21 results • Page 1 of 1
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Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by Guangchuang Yu ★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference by andrebolerbarros ▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by ATpoint ★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference by ATpoint ★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Votes
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
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