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Showing :
BatchEffect
•
reset
0
votes
0
replies
152
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables
DESeq2
BatchEffect
bulkrna-seq
sva-seq
23 days ago • updated 22 days ago
BioinfGuru
▴ 30
2
votes
2
replies
321
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 7 weeks ago by
jessica.mcclintock
• 0 • written 9 weeks ago by
Đình Vinh
• 0
2
votes
2
replies
451
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 7 weeks ago by
jessica.mcclintock
• 0 • written 9 weeks ago by
ttt
• 0
0
votes
0
replies
147
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
10 weeks ago
Shaimaa Gamal
• 0
0
votes
2
replies
389
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 10 weeks ago by
zhouwanding
▴ 20 • written 10 weeks ago by
Seungmin
• 0
2
votes
9
replies
611
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 3 months ago by
James W. MacDonald
66k • written 3 months ago by
Alexandre
• 0
0
votes
2
replies
366
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
3 months ago
catv
• 0
0
votes
8
replies
604
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
4 months ago
michelafrancesconi8
• 0
1
vote
3
replies
488
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 4 months ago by
swbarnes2
★ 1.4k • written 4 months ago by
sap275
▴ 10
0
votes
0
replies
242
views
Can I combine collinear variables into a single value
BatchEffect
limma
4 months ago
Harrsha
• 0
2
votes
1
reply
356
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 5 months ago by
Michael Love
42k • written 5 months ago by
sap275
▴ 10
4
votes
1
reply
600
views
When should I correct for batch effects
BatchEffect
SingleCellExperiment
updated 6 months ago by
James W. MacDonald
66k • written 6 months ago by
NeuroDaniel
▴ 20
0
votes
5
replies
811
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 6 months ago by
ATpoint
★ 4.2k • written 6 months ago by
Xiao
• 0
2
votes
4
replies
844
views
Correct the batch effect in methylation analysis in R
BatchEffect
limma
methylationArrayAnalysis
updated 7 months ago by
Gordon Smyth
51k • written 7 months ago by
kyj2226
• 0
1
vote
4
replies
764
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
8 months ago
Wending
• 0
0
votes
4
replies
751
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 3 months ago by
Michael Love
42k • written 9 months ago by
Crystal571
• 0
0
votes
1
reply
529
views
Batch effect adjust in model matrix
BatchEffect
edgeR
updated 10 months ago by
ATpoint
★ 4.2k • written 10 months ago by
Giuseppe
• 0
3
votes
5
replies
1.1k
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 10 months ago by
ATpoint
★ 4.2k • written 10 months ago by
Shashank
• 0
2
votes
5
replies
1.6k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2
BatchEffect
limma
updated 11 months ago by
Gordon Smyth
51k • written 11 months ago by
Sara
• 0
2
votes
3
replies
1.5k
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 11 months ago by
James W. MacDonald
66k • written 11 months ago by
D-Bug
▴ 10
3
votes
4
replies
1.0k
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
11 months ago
Eva
▴ 10
0
votes
2
replies
735
views
smallRNA-seq analysis batch correction in limma
BatchEffect
limma
12 months ago
Eleonora
• 0
1
vote
1
reply
514
views
Best way to handle batch effects from difference Mice?
RNASeqData
BatchEffect
edgeR
limma
updated 12 months ago by
Gordon Smyth
51k • written 12 months ago by
Sara
• 0
2
votes
3
replies
1.5k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC
RNASeqData
sva
BatchEffect
updated 13 months ago by
ATpoint
★ 4.2k • written 13 months ago by
amnahsiddiqa
▴ 10
0
votes
0
replies
460
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
13 months ago
amnahsiddiqa
▴ 10
1
vote
1
reply
579
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 13 months ago by
ATpoint
★ 4.2k • written 13 months ago by
khaserdene99
• 0
2
votes
5
replies
1.4k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 3 months ago by
Ashley
• 0 • written 13 months ago by
zxc741xb
• 0
1
vote
2
replies
1.1k
views
Batch effect between biological replicates
BatchEffect
DESeq2
14 months ago
gtechbio
▴ 10
0
votes
4
replies
1.1k
views
Combine RNA-seq
BatchEffect
R
rnaseq
updated 15 months ago by
swbarnes2
★ 1.4k • written 15 months ago by
Young Tae
• 0
2
votes
4
replies
1.7k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2
BatchEffect
tpm
fpkm
15 months ago
vk
• 0
2
votes
2
replies
1.0k
views
Error in checkFullRank(modelMatrix)
DESeq2
BatchEffect
DifferentialExpression
updated 15 months ago by
ATpoint
★ 4.2k • written 15 months ago by
AZ
▴ 30
2
votes
3
replies
1.1k
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 16 months ago by
ATpoint
★ 4.2k • written 16 months ago by
suphamon.j
▴ 20
0
votes
1
reply
718
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 11 months ago by
wrab425
• 0 • written 16 months ago by
snijesh
▴ 20
3
votes
2
replies
879
views
Batch question Bulk RNA-Seq
BatchEffect
RNASeq
16 months ago
chf
• 0
2
votes
1
reply
1.8k
views
DESeq2 design after combatseq batch correction
DESeq2
BatchEffect
updated 17 months ago by
ATpoint
★ 4.2k • written 17 months ago by
Tyroone
• 0
0
votes
1
reply
542
views
Analysis with Batch correction
DESeq2
BatchEffect
updated 17 months ago by
Michael Love
42k • written 17 months ago by
giulia.lopatriello
• 0
1
vote
1
reply
857
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR
model.matrix
BatchEffect
updated 17 months ago by
James W. MacDonald
66k • written 17 months ago by
greta
• 0
5
votes
2
replies
876
views
Sva and batch effect
limma
BatchEffect
sva
updated 18 months ago by
Gordon Smyth
51k • written 18 months ago by
Lenny186
• 0
1
vote
1
reply
2.1k
views
batch effect correction before DESeq2 analysis
DESeq2
BatchEffect
updated 18 months ago by
ATpoint
★ 4.2k • written 18 months ago by
luca.s
▴ 50
0
votes
0
replies
852
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
18 months ago
Zhijie
• 0
1
vote
0
replies
782
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran
Normalization
scRNA
BatchEffect
19 months ago
r_grau
▴ 10
1
vote
2
replies
993
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2
BatchEffect
RNASeq
updated 21 months ago by
swbarnes2
★ 1.4k • written 21 months ago by
Flavio
• 0
3
votes
10
replies
2.1k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2
BatchEffect
fold
21 months ago
eve.olszanowski
• 0
1
vote
2
replies
860
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2
BatchEffect
22 months ago • updated 21 months ago
annamariabugaj
▴ 10
0
votes
1
reply
1.1k
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 23 months ago by
Michael Love
42k • written 23 months ago by
estafana.t98
• 0
0
votes
1
reply
957
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData
BatchEffect
r
limma
updated 24 months ago by
Gordon Smyth
51k • written 24 months ago by
mfaleevs
• 0
1
vote
1
reply
778
views
RNA-Seq normalization and batch effect removal
RNASeq
BatchEffect
DESeq2
updated 2.1 years ago by
Michael Love
42k • written 2.1 years ago by
Alexandre
• 0
6
votes
7
replies
2.1k
views
Batch effect with one sample being in two batches
BatchEffect
DESeq2
2.1 years ago
lmrogers34
▴ 10
2
votes
1
reply
1.5k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma
BatchEffect
updated 2.2 years ago by
Gordon Smyth
51k • written 2.2 years ago by
nhaus
▴ 50
0
votes
1
reply
1.1k
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 2.3 years ago by
Gordon Smyth
51k • written 2.3 years ago by
Mageiros
• 0
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Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
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