Showing : batcheffect • reset
6
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4
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7.9k
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How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 21 months ago by • 0 • written 2.6 years ago by ▴ 10
2
votes
4
replies
4.2k
views
edgeR and batch effect correction for differential analysis
edger limma r rnaseq batcheffect
updated 4.4 years ago by 63k • written 4.4 years ago by • 0
6
votes
4
replies
3.8k
views
Merge different datasets and perform differential expression analysis in limma
insilicomerging batcheffect limma differential gene expression bioconductor
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 810
3
votes
6
replies
2.9k
views
RNAseq multifactor experiment limma design with patient and batch effects
limma rnaseq batcheffect
updated 8.3 years ago by • 0 • written 8.9 years ago by ▴ 10
2
votes
3
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2.7k
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Questions in limma about multifactorial design and possible batch effect correction
limma batcheffect batcheffectcorrection multiple factor design
updated 8.4 years ago by 63k • written 8.4 years ago by ▴ 810
1
vote
5
replies
1.9k
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Deseq2 - removing batch effect
BatchEffect DESeq2
updated 2.4 years ago by 3.8k • written 2.4 years ago by • 0
3
votes
6
replies
1.9k
views
is it necessary to check batch effect in this case? and how to?
svaseq combat sva RANseq batcheffect removebatcheffect
updated 6.9 years ago by ▴ 50 • written 7.0 years ago by ▴ 10
1
vote
15
replies
1.9k
views
between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
2.5 years ago demisa • 0
4
votes
10
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1.7k
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Subject: Strange glitch in Voom curve resulting from batch effects
limma voom batcheffect covariate
updated 6.4 years ago by 48k • written 6.4 years ago by ▴ 20
0
votes
3
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1.7k
views
Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 2.1 years ago by 40k • written 2.1 years ago by • 0
1
vote
5
replies
1.6k
views
Appropriate merge of batches of the same array to create a final total ExpressionSet
frma bioconductor batcheffect Primeview insilicomerging
updated 8.5 years ago by ▴ 830 • written 8.5 years ago by ▴ 810
2
votes
1
reply
1.5k
views
EdgeR: Accounting for batch effects in a pairwise analysis
paired batcheffect
updated 8.7 years ago by 48k • written 8.7 years ago by • 0
1
vote
6
replies
1.3k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 4.4 years ago by 63k • written 4.4 years ago by ▴ 110
3
votes
10
replies
1.2k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
12 months ago • updated 11 months ago eve.olszanowski • 0
6
votes
7
replies
1.2k
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
16 months ago • updated 15 months ago lmrogers34 ▴ 10
0
votes
0
replies
1.1k
views
Quantiles from virtualArray example without batcheffect removal are all the same
Microarray BatchEffect hgu133plus2 hgug4112a virtualArray Microarray BatchEffect hgug4112a
10.5 years ago Daniel Emden ▴ 10
1
vote
1
reply
1.1k
views
DESeq2 batch effects
BatchEffect DESeq2 RNASeq
updated 2.9 years ago by 40k • written 2.9 years ago by ▴ 40
6
votes
6
replies
1.0k
views
Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
23 months ago ary.lech ▴ 10
1
vote
7
replies
921
views
Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 19 months ago by 63k • written 19 months ago by ▴ 10
1
vote
5
replies
915
views
Group Specific Condition Query
deseq2 deseq batcheffect
updated 5.1 years ago by 40k • written 5.1 years ago by ▴ 10
2
votes
2
replies
898
views
Addressing the batch effect in multifactor experiment
edgeR BatchEffect RNASeq
updated 2.8 years ago by ▴ 300 • written 2.9 years ago by ▴ 10
2
votes
1
reply
828
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 16 months ago by 48k • written 16 months ago by • 0
2
votes
4
replies
823
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 4 weeks ago by 40k • written 2.3 years ago by • 0
0
votes
2
replies
822
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 21 months ago by 13k • written 21 months ago by • 0
1
vote
1
reply
803
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 2.9 years ago by ★ 28k • written 2.9 years ago by • 0
2
votes
2
replies
784
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 2.6 years ago by ★ 3.4k • written 2.6 years ago by • 0
1
vote
1
reply
780
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 19 months ago by ★ 3.4k • written 19 months ago by • 0
1
vote
3
replies
773
views
Limma: Differential expression with two batch effects , location and batch.
duplicatecorrelation BatchEffect limma corfit
updated 2.9 years ago by 48k • written 2.9 years ago by • 0
0
votes
2
replies
758
views
extract certain subpopulation of MouseGastrulationData
MouseGastrulationData Normalization BatchEffect
updated 2.9 years ago by ▴ 40 • written 2.9 years ago by ▴ 120
0
votes
1
reply
741
views
Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 2.9 years ago by 3.8k • written 2.9 years ago by • 0
2
votes
2
replies
710
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn batchelor BatchEffect
2.0 years ago p.joshi ▴ 40
1
vote
2
replies
676
views
Is 100K genes too many to run ComBat_seq on?
RNASeqRData combat_Seq BatchEffect
2.0 years ago • updated 20 months ago zeegzaag • 0
0
votes
2
replies
675
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
23 months ago m.glymenaki • 0
1
vote
1
reply
653
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 8 months ago by ★ 3.4k • written 8 months ago by ▴ 50
0
votes
1
reply
641
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 13 months ago by 40k • written 13 months ago by • 0
2
votes
4
replies
636
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
5 months ago vk • 0
0
votes
1
reply
612
views
Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data RNASeqR Normalization BatchEffect
updated 24 months ago by 63k • written 24 months ago by • 0
0
votes
1
reply
601
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 17 months ago by 48k • written 17 months ago by • 0
0
votes
0
replies
567
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
2.9 years ago hamza_karakurt ▴ 50
0
votes
1
reply
563
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 14 months ago by 48k • written 14 months ago by • 0
1
vote
2
replies
514
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 11 months ago by ★ 1.3k • written 11 months ago by • 0
1
vote
2
replies
510
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
12 months ago annamariabugaj ▴ 10
1
vote
1
reply
508
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 16 months ago by 40k • written 16 months ago by • 0
5
votes
2
replies
474
views
Sva and batch effect
limma BatchEffect sva
updated 8 months ago by 48k • written 8 months ago by • 0
1
vote
2
replies
470
views
Batch effect between biological replicates
BatchEffect DESeq2
4 months ago gtechbio ▴ 10
2
votes
3
replies
458
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 3 months ago by 63k • written 3 months ago by • 0
1
vote
3
replies
455
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 3 months ago by ★ 3.4k • written 3 months ago by • 0
2
votes
1
reply
444
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 7 months ago by ★ 3.4k • written 7 months ago by • 0
2
votes
3
replies
414
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 6 months ago by ★ 3.4k • written 6 months ago by ▴ 10
1
vote
1
reply
410
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 7 months ago by 63k • written 7 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Exporting DESeq2 filtered results by James W. MacDonald 63k
I am interested to know what part of my response you found rude. I asked nicely that you don't add to ancient posts, said your post isn't r…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
> I can imagine writing a sparse high-dimensional array in HDF5, but I'm still not sure how to implement the part where it is read and imme…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Not in BioC 3.18. At some point (e.g. in 6 months) they will be deprecated, then 6 months later (i.e. in 1 year) they will be defunct, then…
Comment: Biostrings error at retrieving protein sequences by Hervé Pagès 16k
Yes, but you need to put the clean names back on the AAStringSet object: ``` names(protein_sequences) <- gsub(" .*", "", names(protein_sequ…
Comment: Exporting DESeq2 filtered results by camillab. ▴ 10
thanks! I didn't`t notice that. I will cancel it now!
Votes
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
A: BiomaRt Arabidopsis genome unavailable
Answer: enrichKEGG
A: Effect of lfcThreshold on p-value in DESeq2
Comment: Mixed up sample info with plotPCA
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