Showing : batcheffect • reset
6
votes
4
replies
11k
views
How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 2.3 years ago by • 0 • written 3.1 years ago by ▴ 10
2
votes
4
replies
4.9k
views
edgeR and batch effect correction for differential analysis
edger limma r rnaseq batcheffect
updated 5.0 years ago by 65k • written 5.0 years ago by • 0
6
votes
4
replies
4.0k
views
Merge different datasets and perform differential expression analysis in limma
insilicomerging batcheffect limma differential gene expression bioconductor
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 830
3
votes
6
replies
3.0k
views
RNAseq multifactor experiment limma design with patient and batch effects
limma rnaseq batcheffect
updated 8.9 years ago by • 0 • written 9.5 years ago by ▴ 10
2
votes
3
replies
2.8k
views
Questions in limma about multifactorial design and possible batch effect correction
limma batcheffect batcheffectcorrection multiple factor design
updated 9.0 years ago by 65k • written 9.0 years ago by ▴ 830
1
vote
5
replies
2.6k
views
Deseq2 - removing batch effect
BatchEffect DESeq2
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by • 0
1
vote
15
replies
2.5k
views
between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
3.0 years ago demisa • 0
0
votes
3
replies
2.3k
views
Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
3
votes
6
replies
2.2k
views
is it necessary to check batch effect in this case? and how to?
svaseq combat sva RANseq batcheffect removebatcheffect
updated 7.5 years ago by ▴ 50 • written 7.5 years ago by ▴ 10
4
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10
replies
2.0k
views
Subject: Strange glitch in Voom curve resulting from batch effects
limma voom batcheffect covariate
updated 7.0 years ago by 50k • written 7.0 years ago by ▴ 20
1
vote
5
replies
1.9k
views
Appropriate merge of batches of the same array to create a final total ExpressionSet
frma bioconductor batcheffect Primeview insilicomerging
updated 9.0 years ago by ▴ 830 • written 9.0 years ago by ▴ 830
3
votes
10
replies
1.9k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
18 months ago eve.olszanowski • 0
6
votes
7
replies
1.8k
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
22 months ago lmrogers34 ▴ 10
1
vote
6
replies
1.6k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 110
1
vote
1
reply
1.6k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 15 months ago by ★ 4.0k • written 15 months ago by ▴ 50
2
votes
1
reply
1.6k
views
EdgeR: Accounting for batch effects in a pairwise analysis
paired batcheffect
updated 9.2 years ago by 50k • written 9.2 years ago by • 0
2
votes
4
replies
1.4k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
12 months ago vk • 0
6
votes
6
replies
1.4k
views
Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
2.5 years ago ary.lech ▴ 10
2
votes
1
reply
1.4k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 14 months ago by ★ 4.0k • written 14 months ago by • 0
1
vote
1
reply
1.3k
views
DESeq2 batch effects
BatchEffect DESeq2 RNASeq
updated 3.5 years ago by 41k • written 3.5 years ago by ▴ 40
2
votes
1
reply
1.3k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 23 months ago by 50k • written 23 months ago by ▴ 30
1
vote
7
replies
1.3k
views
Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 2.2 years ago by 65k • written 2.2 years ago by ▴ 10
2
votes
5
replies
1.3k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 8 months ago by 50k • written 8 months ago by • 0
0
votes
0
replies
1.3k
views
Quantiles from virtualArray example without batcheffect removal are all the same
Microarray BatchEffect hgu133plus2 hgug4112a virtualArray Microarray BatchEffect hgug4112a
11.0 years ago Daniel Emden ▴ 10
2
votes
4
replies
1.2k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 7 months ago by 41k • written 2.9 years ago by • 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 9 days ago by • 0 • written 10 months ago by • 0
2
votes
3
replies
1.1k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 10 months ago by ★ 4.0k • written 10 months ago by ▴ 10
1
vote
5
replies
1.1k
views
Group Specific Condition Query
deseq2 deseq batcheffect
updated 5.7 years ago by 41k • written 5.7 years ago by ▴ 10
1
vote
1
reply
1.1k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 2.2 years ago by ★ 4.0k • written 2.2 years ago by ▴ 30
2
votes
3
replies
1.1k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 8 months ago by 65k • written 8 months ago by ▴ 10
0
votes
2
replies
1.0k
views
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
2
votes
2
replies
1.0k
views
Addressing the batch effect in multifactor experiment
edgeR BatchEffect RNASeq
updated 3.4 years ago by ▴ 350 • written 3.4 years ago by ▴ 10
1
vote
1
reply
997
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 3.4 years ago by ★ 28k • written 3.5 years ago by • 0
2
votes
2
replies
974
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 3.2 years ago by ★ 4.0k • written 3.2 years ago by • 0
1
vote
2
replies
961
views
Batch effect between biological replicates
BatchEffect DESeq2
11 months ago gtechbio ▴ 10
2
votes
2
replies
958
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn batchelor BatchEffect
2.6 years ago p.joshi ▴ 40
0
votes
1
reply
956
views
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
3
replies
943
views
Limma: Differential expression with two batch effects , location and batch.
duplicatecorrelation BatchEffect limma corfit
updated 3.4 years ago by 50k • written 3.4 years ago by • 0
0
votes
1
reply
936
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
votes
2
replies
928
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
2.5 years ago m.glymenaki • 0
0
votes
2
replies
923
views
extract certain subpopulation of MouseGastrulationData
MouseGastrulationData Normalization BatchEffect
updated 3.4 years ago by ▴ 90 • written 3.4 years ago by ▴ 120
0
votes
1
reply
916
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.0 years ago by 50k • written 2.0 years ago by • 0
0
votes
4
replies
886
views
Combine RNA-seq
BatchEffect R rnaseq
updated 12 months ago by ★ 1.3k • written 12 months ago by • 0
1
vote
2
replies
880
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 18 months ago by ★ 1.3k • written 18 months ago by • 0
2
votes
3
replies
879
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.0k • written 13 months ago by ▴ 20
1
vote
2
replies
877
views
Is 100K genes too many to run ComBat_seq on?
RNASeqRData combat_Seq BatchEffect
2.6 years ago • updated 2.3 years ago zeegzaag • 0
0
votes
1
reply
863
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 21 months ago by 50k • written 21 months ago by • 0
2
votes
2
replies
857
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 12 months ago by ★ 4.0k • written 12 months ago by ▴ 30
3
votes
4
replies
854
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
8 months ago Eva ▴ 10
0
votes
1
reply
830
views
Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data RNASeqR Normalization BatchEffect
updated 2.5 years ago by 65k • written 2.5 years ago by ▴ 20
50 results • Page 1 of 1
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 30
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
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Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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