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Showing :
batcheffect
•
reset
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
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
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
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
Aaron Lun
★ 28k • written 8.2 years ago by
svlachavas
▴ 810
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
4
votes
10
replies
1.7k
views
Subject: Strange glitch in Voom curve resulting from batch effects
limma
voom
batcheffect
covariate
updated 6.4 years ago by
Gordon Smyth
48k • written 6.4 years ago by
raf4
▴ 20
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
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
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
3
votes
2
replies
375
views
Batch question Bulk RNA-Seq
BatchEffect
RNASeq
6 months ago
chf
• 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
Jakub
▴ 50 • written 7.0 years ago by
amoltej
▴ 10
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
robert.maughan
• 0 • written 8.9 years ago by
cfreije
▴ 10
2
votes
3
replies
2.7k
views
Questions in limma about multifactorial design and possible batch effect correction
limma
batcheffect
batcheffectcorrection
multiple factor design
updated 8.4 years ago by
James W. MacDonald
63k • written 8.4 years ago by
svlachavas
▴ 810
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
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
2
votes
1
reply
1.5k
views
EdgeR: Accounting for batch effects in a pairwise analysis
paired
batcheffect
updated 8.7 years ago by
Gordon Smyth
48k • written 8.7 years ago by
cinderelliedoll
• 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
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
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
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
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
2
votes
2
replies
402
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
4
replies
4.2k
views
edgeR and batch effect correction for differential analysis
edger
limma
r
rnaseq
batcheffect
updated 4.4 years ago by
James W. MacDonald
63k • written 4.4 years ago by
m93
• 0
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
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
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
3
replies
773
views
Limma: Differential expression with two batch effects , location and batch.
duplicatecorrelation
BatchEffect
limma
corfit
updated 2.9 years ago by
Gordon Smyth
48k • written 2.9 years ago by
Katherine
• 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
Matthew McCall
▴ 830 • written 8.5 years ago by
svlachavas
▴ 810
1
vote
5
replies
915
views
Group Specific Condition Query
deseq2
deseq
batcheffect
updated 5.1 years ago by
Michael Love
40k • written 5.1 years ago by
bdy8
▴ 10
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
James W. MacDonald
63k • written 4.4 years ago by
Biologist
▴ 110
1
vote
1
reply
1.1k
views
DESeq2 batch effects
BatchEffect
DESeq2
RNASeq
updated 2.9 years ago by
Michael Love
40k • written 2.9 years ago by
igor
▴ 40
1
vote
1
reply
803
views
Combining treatment and control batches for analysis
scRNAseq
scRNA
batchelor
BatchEffect
updated 2.9 years ago by
Aaron Lun
★ 28k • written 2.9 years ago by
Adrien
• 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
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
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
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
1
vote
2
replies
470
views
Batch effect between biological replicates
BatchEffect
DESeq2
4 months ago
gtechbio
▴ 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
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
1
reply
508
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
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
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
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
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
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
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
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
514
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
0
votes
2
replies
250
views
smallRNA-seq analysis batch correction in limma
BatchEffect
limma
10 weeks ago
Eleonora
• 0
0
votes
1
reply
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
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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