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batcheffect
•
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0
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150
views
Batch effect adjust in model matrix
BatchEffect
edgeR
updated 6 days ago by
ATpoint
★ 3.4k • written 6 days ago by
Giuseppe
• 0
3
votes
5
replies
229
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 20 days ago by
ATpoint
★ 3.4k • written 21 days ago by
Shashank
• 0
2
votes
5
replies
364
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2
BatchEffect
limma
updated 7 weeks ago by
Gordon Smyth
48k • written 7 weeks ago by
Sara
• 0
1
vote
3
replies
255
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 7 weeks ago by
James W. MacDonald
63k • written 7 weeks ago by
D-Bug
• 0
3
votes
4
replies
406
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
8 weeks ago • updated 7 weeks ago
Eva
▴ 10
0
votes
2
replies
250
views
smallRNA-seq analysis batch correction in limma
BatchEffect
limma
10 weeks ago
Eleonora
• 0
1
vote
1
reply
244
views
Best way to handle batch effects from difference Mice?
RNASeqData
BatchEffect
edgeR
limma
updated 12 weeks ago by
Gordon Smyth
48k • written 12 weeks ago by
Sara
• 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
ATpoint
★ 3.4k • written 3 months ago by
amnahsiddiqa
• 0
0
votes
0
replies
166
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
3 months ago
amnahsiddiqa
• 0
1
vote
1
reply
192
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 3 months ago by
ATpoint
★ 3.4k • written 3 months ago by
khaserdene99
• 0
2
votes
3
replies
458
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 3 months ago by
James W. MacDonald
63k • written 3 months ago by
zxc741xb
• 0
1
vote
2
replies
470
views
Batch effect between biological replicates
BatchEffect
DESeq2
4 months ago
gtechbio
▴ 10
0
votes
4
replies
402
views
Combine RNA-seq
BatchEffect
R
rnaseq
updated 5 months ago by
swbarnes2
★ 1.3k • written 5 months ago by
Young Tae
• 0
2
votes
4
replies
637
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2
BatchEffect
tpm
fpkm
5 months ago
vk
• 0
2
votes
2
replies
403
views
Error in checkFullRank(modelMatrix)
DESeq2
BatchEffect
DifferentialExpression
updated 5 months ago by
ATpoint
★ 3.4k • written 5 months ago by
AZ
▴ 30
2
votes
3
replies
414
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 6 months ago by
ATpoint
★ 3.4k • written 6 months ago by
suphamon.j
▴ 10
0
votes
1
reply
282
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 6 weeks ago by
wrab425
• 0 • written 6 months ago by
snijesh
▴ 20
3
votes
2
replies
376
views
Batch question Bulk RNA-Seq
BatchEffect
RNASeq
6 months ago
chf
• 0
2
votes
1
reply
444
views
DESeq2 design after combatseq batch correction
DESeq2
BatchEffect
updated 7 months ago by
ATpoint
★ 3.4k • written 7 months ago by
Tyroone
• 0
0
votes
1
reply
305
views
Analysis with Batch correction
DESeq2
BatchEffect
updated 7 months ago by
Michael Love
40k • written 7 months ago by
giulia.lopatriello
• 0
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
James W. MacDonald
63k • written 7 months ago by
greta
• 0
5
votes
2
replies
474
views
Sva and batch effect
limma
BatchEffect
sva
updated 8 months ago by
Gordon Smyth
48k • written 8 months ago by
Lenny186
• 0
1
vote
1
reply
653
views
batch effect correction before DESeq2 analysis
DESeq2
BatchEffect
updated 8 months ago by
ATpoint
★ 3.4k • written 8 months ago by
luca.s
▴ 50
0
votes
0
replies
351
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
9 months ago
Zhijie
• 0
1
vote
0
replies
337
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran
Normalization
scRNA
BatchEffect
9 months ago
r_grau
▴ 10
1
vote
2
replies
515
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2
BatchEffect
RNASeq
updated 11 months ago by
swbarnes2
★ 1.3k • written 11 months ago by
Flavio
• 0
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
1
vote
2
replies
511
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2
BatchEffect
12 months ago
annamariabugaj
▴ 10
0
votes
1
reply
641
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 13 months ago by
Michael Love
40k • written 13 months ago by
estafana.t98
• 0
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
Gordon Smyth
48k • written 14 months ago by
mfaleevs
• 0
1
vote
1
reply
509
views
RNA-Seq normalization and batch effect removal
RNASeq
BatchEffect
DESeq2
updated 16 months ago by
Michael Love
40k • written 16 months ago by
Alexandre
• 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
2
votes
1
reply
828
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma
BatchEffect
updated 16 months ago by
Gordon Smyth
48k • written 16 months ago by
nhaus
• 0
0
votes
1
reply
601
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 17 months ago by
Gordon Smyth
48k • written 17 months ago by
Mageiros
• 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
ATpoint
★ 3.4k • written 19 months ago by
nhaus
• 0
0
votes
0
replies
351
views
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
19 months ago
Ety
• 0
1
vote
7
replies
921
views
Comparison DESeq results using different model
Batch
BatchEffect
DESeq2
updated 19 months ago by
James W. MacDonald
63k • written 19 months ago by
dequattro.concetta
▴ 10
0
votes
2
replies
823
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch
RNASeq
BatchEffect
DESeq2
updated 21 months ago by
Steve Lianoglou
13k • written 21 months ago by
Jonas
• 0
0
votes
2
replies
675
views
Design formula in DESeq2
model
BatchEffect
hidden
Design
DESeq2
23 months ago
m.glymenaki
• 0
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
0
votes
1
reply
613
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
James W. MacDonald
63k • written 24 months ago by
bhandary.8590
• 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
3
replies
1.7k
views
Different PCA results when using rlog and vst transformations
vsn
DESeq2
rlog
BatchEffect
updated 2.1 years ago by
Michael Love
40k • written 2.1 years ago by
Diamond
• 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
Michael Love
40k • written 2.3 years ago by
athiebaut
• 0
1
vote
5
replies
1.9k
views
Deseq2 - removing batch effect
BatchEffect
DESeq2
updated 2.4 years ago by
Kevin Blighe
3.8k • written 2.4 years ago by
vinisha
• 0
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
6
votes
4
replies
7.9k
views
How to use combat in order to remove batch effects?
BatchEffect
DESeq2
RNASeqData
updated 21 months ago by
BioNovice247
• 0 • written 2.6 years ago by
Emma
▴ 10
2
votes
2
replies
784
views
Preprocessing Issue
sva
RNASeq
Preprocessing
Normalization
BatchEffect
updated 2.6 years ago by
ATpoint
★ 3.4k • written 2.6 years ago by
MOHAMMAD
• 0
2
votes
2
replies
898
views
Addressing the batch effect in multifactor experiment
edgeR
BatchEffect
RNASeq
updated 2.8 years ago by
SamGG
▴ 300 • written 2.9 years ago by
anikng
▴ 10
50 results • Page
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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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