Showing : batcheffect • reset
1
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269
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Batch effect between biological replicates
BatchEffect DESeq2
15 days ago • updated 12 days ago gtechbio ▴ 10
0
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4
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212
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Combine RNA-seq
BatchEffect R rnaseq
updated 5 weeks ago by ★ 1.2k • written 5 weeks ago by • 0
2
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4
replies
237
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How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
6 weeks ago vk • 0
2
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2
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192
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Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 6 weeks ago by ★ 2.8k • written 6 weeks ago by ▴ 30
1
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3
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198
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 9 weeks ago by ★ 2.8k • written 11 weeks ago by • 0
0
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0
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124
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How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
11 weeks ago snijesh ▴ 20
3
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2
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173
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Batch question Bulk RNA-Seq
BatchEffect RNASeq
11 weeks ago chf • 0
2
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1
reply
159
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DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 3 months ago by ★ 2.8k • written 3 months ago by • 0
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1
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186
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Analysis with Batch correction
DESeq2 BatchEffect
updated 3 months ago by 40k • written 3 months ago by • 0
1
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1
reply
208
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 3 months ago by 62k • written 3 months ago by • 0
5
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2
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285
views
Sva and batch effect
limma BatchEffect sva
updated 3 months ago by 47k • written 3 months ago by • 0
1
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1
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284
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batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 4 months ago by ★ 2.8k • written 4 months ago by ▴ 40
0
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0
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171
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
4 months ago Zhijie • 0
1
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0
replies
208
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Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
5 months ago r_grau ▴ 10
1
vote
2
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343
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Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 7 months ago by ★ 1.2k • written 7 months ago by • 0
3
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10
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848
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Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
7 months ago eve.olszanowski • 0
0
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2
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348
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Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
7 months ago annamariabugaj ▴ 10
0
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1
reply
433
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 9 months ago by 40k • written 9 months ago by • 0
0
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1
reply
389
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 9 months ago by 47k • written 10 months ago by • 0
1
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1
reply
415
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 11 months ago by 40k • written 11 months ago by • 0
6
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7
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845
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
11 months ago lmrogers34 ▴ 10
2
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1
reply
618
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removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 12 months ago by 47k • written 12 months ago by • 0
0
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1
reply
404
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 13 months ago by 47k • written 13 months ago by • 0
1
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1
reply
579
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 15 months ago by ★ 2.8k • written 15 months ago by • 0
0
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0
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279
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Is it possible to do batch correction on Ht-Seq raw counts instead of using normalized counts? What's the difference?
Normalisedcounts Rawcounts Ht-SeqRNAData BatchEffect
15 months ago Ety • 0
1
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7
replies
691
views
Comparison DESeq results using different model
Batch BatchEffect DESeq2
updated 15 months ago by 62k • written 15 months ago by ▴ 10
0
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2
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688
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 17 months ago by 13k • written 17 months ago by • 0
0
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2
replies
522
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
19 months ago m.glymenaki • 0
6
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6
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773
views
Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
19 months ago ary.lech ▴ 10
0
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1
reply
474
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Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data RNASeqR Normalization BatchEffect
updated 19 months ago by 62k • written 19 months ago by • 0
2
votes
2
replies
578
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn batchelor BatchEffect
20 months ago p.joshi ▴ 40
1
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2
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559
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Is 100K genes too many to run ComBat_seq on?
RNASeqRData combat_Seq BatchEffect
20 months ago • updated 16 months ago zeegzaag • 0
0
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3
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1.3k
views
Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 21 months ago by 40k • written 21 months ago by • 0
2
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3
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621
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RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 23 months ago by • 0 • written 24 months ago by • 0
1
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5
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1.5k
views
Deseq2 - removing batch effect
BatchEffect DESeq2
updated 2.1 years ago by 3.8k • written 2.1 years ago by • 0
1
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15
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1.4k
views
between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
2.1 years ago demisa • 0
6
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4
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6.2k
views
How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
updated 16 months ago by • 0 • written 2.2 years ago by ▴ 10
2
votes
2
replies
621
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 2.3 years ago by ★ 2.8k • written 2.3 years ago by • 0
2
votes
2
replies
788
views
Addressing the batch effect in multifactor experiment
edgeR BatchEffect RNASeq
updated 2.5 years ago by ▴ 290 • written 2.5 years ago by ▴ 10
1
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3
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629
views
Limma: Differential expression with two batch effects , location and batch.
duplicatecorrelation BatchEffect limma corfit
updated 2.5 years ago by 47k • written 2.5 years ago by • 0
0
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1
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625
views
Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 2.5 years ago by 3.8k • written 2.5 years ago by • 0
0
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2
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622
views
extract certain subpopulation of MouseGastrulationData
MouseGastrulationData Normalization BatchEffect
updated 2.5 years ago by ▴ 40 • written 2.5 years ago by ▴ 120
1
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1
reply
701
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 2.5 years ago by ★ 28k • written 2.5 years ago by • 0
1
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1
reply
917
views
DESeq2 batch effects
BatchEffect DESeq2 RNASeq
updated 2.5 years ago by 40k • written 2.5 years ago by ▴ 40
0
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0
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467
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
2.6 years ago hamza_karakurt ▴ 50
2
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4
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3.7k
views
edgeR and batch effect correction for differential analysis
edger limma r rnaseq batcheffect
updated 4.0 years ago by 62k • written 4.0 years ago by • 0
1
vote
6
replies
1.1k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 4.0 years ago by 62k • written 4.0 years ago by ▴ 110
1
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5
replies
795
views
Group Specific Condition Query
deseq2 deseq batcheffect
updated 4.8 years ago by 40k • written 4.8 years ago by ▴ 10
4
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10
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1.5k
views
Subject: Strange glitch in Voom curve resulting from batch effects
limma voom batcheffect covariate
updated 6.1 years ago by 47k • written 6.1 years ago by ▴ 20
3
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6
replies
1.7k
views
is it necessary to check batch effect in this case? and how to?
svaseq combat sva RANseq batcheffect removebatcheffect
updated 6.6 years ago by ▴ 50 • written 6.6 years ago by ▴ 10
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Comment: BiocGenerics binary is outdated for macOS ARM by jennifer.wokaty ▴ 60
Thanks, Mike, for posting about this and thanks to Lori for noticing the lock. I removed it and RProtoBufLib passes R CMD check. Unfortunat…
Comment: BiocGenerics binary is outdated for macOS ARM by Michael Steinbaugh ▴ 90
Ah thanks for the update. Yeah I see that the flowClust release is the culprit: https://www.bioconductor.org/packages/release/bioc/html/flo…
Comment: Submitting BSgenome package for a new assembly by Manish • 0
Thanks for the info. This is very helpful. -Manish
Comment: Merge 2 accounts, or delete 1 account. by shepherl 3.5k
are you talking specifically on the support site or elsewhere also?
Comment: BiocGenerics binary is outdated for macOS ARM by shepherl 3.5k
That is because it is failing from dependencies not being available. https://bioconductor.org/checkResults/3.17/bioc-mac-arm64-LATEST/BiocG…
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flowCore: using read.FCS with which.lines is not time efficient?
Comment: BiocGenerics binary is outdated for macOS ARM
Comment: Submitting BSgenome package for a new assembly
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