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BatchEffect
•
reset
0
votes
8
replies
256
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
11 days ago
michelafrancesconi8
• 0
1
vote
3
replies
234
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 14 days ago by
swbarnes2
★ 1.3k • written 17 days ago by
sap275
▴ 10
0
votes
0
replies
104
views
Can I combine collinear variables into a single value
BatchEffect
limma
18 days ago
Harrsha
• 0
2
votes
1
reply
179
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 21 days ago by
Michael Love
41k • written 22 days ago by
sap275
▴ 10
1
vote
5
replies
291
views
RLE plots before and after RUVg correction are the same
RUVSeq
RUVcorr
RNASeqData
BatchEffect
DifferentialExpression
updated 27 days ago by
James W. MacDonald
65k • written 28 days ago by
Shaimaa Gamal
• 0
0
votes
1
reply
172
views
When should I correct for batch effects
BatchEffect
SingleCellExperiment
updated 7 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
NeuroDaniel
• 0
0
votes
5
replies
428
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 10 weeks ago by
ATpoint
★ 3.9k • written 10 weeks ago by
Xiao
• 0
2
votes
4
replies
516
views
Correct the batch effect in methylation analysis in R
BatchEffect
limma
methylationArrayAnalysis
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
kyj2226
• 0
1
vote
4
replies
542
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
4 months ago
Wending
• 0
0
votes
2
replies
423
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
4 months ago
Crystal571
• 0
0
votes
1
reply
385
views
Batch effect adjust in model matrix
BatchEffect
edgeR
updated 5 months ago by
ATpoint
★ 3.9k • written 5 months ago by
Giuseppe
• 0
3
votes
5
replies
686
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 6 months ago by
ATpoint
★ 3.9k • written 6 months ago by
Shashank
• 0
2
votes
5
replies
1.1k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2
BatchEffect
limma
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
Sara
• 0
2
votes
3
replies
894
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 months ago by
James W. MacDonald
65k • written 7 months ago by
D-Bug
▴ 10
3
votes
4
replies
780
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
7 months ago
Eva
▴ 10
0
votes
2
replies
544
views
smallRNA-seq analysis batch correction in limma
BatchEffect
limma
8 months ago
Eleonora
• 0
1
vote
1
reply
420
views
Best way to handle batch effects from difference Mice?
RNASeqData
BatchEffect
edgeR
limma
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
Sara
• 0
2
votes
3
replies
995
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC
RNASeqData
sva
BatchEffect
updated 8 months ago by
ATpoint
★ 3.9k • written 8 months ago by
amnahsiddiqa
• 0
0
votes
0
replies
348
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
8 months ago
amnahsiddiqa
• 0
1
vote
1
reply
437
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 8 months ago by
ATpoint
★ 3.9k • written 8 months ago by
khaserdene99
• 0
2
votes
4
replies
975
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 4 months ago by
melissawimmer219
• 0 • written 9 months ago by
zxc741xb
• 0
1
vote
2
replies
875
views
Batch effect between biological replicates
BatchEffect
DESeq2
10 months ago
gtechbio
▴ 10
0
votes
4
replies
789
views
Combine RNA-seq
BatchEffect
R
rnaseq
updated 10 months ago by
swbarnes2
★ 1.3k • written 10 months ago by
Young Tae
• 0
2
votes
4
replies
1.3k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2
BatchEffect
tpm
fpkm
11 months ago
vk
• 0
2
votes
2
replies
784
views
Error in checkFullRank(modelMatrix)
DESeq2
BatchEffect
DifferentialExpression
updated 11 months ago by
ATpoint
★ 3.9k • written 11 months ago by
AZ
▴ 30
2
votes
3
replies
798
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 12 months ago by
ATpoint
★ 3.9k • written 12 months ago by
suphamon.j
▴ 20
0
votes
1
reply
553
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 7 months ago by
wrab425
• 0 • written 12 months ago by
snijesh
▴ 20
3
votes
2
replies
664
views
Batch question Bulk RNA-Seq
BatchEffect
RNASeq
12 months ago
chf
• 0
2
votes
1
reply
1.2k
views
DESeq2 design after combatseq batch correction
DESeq2
BatchEffect
updated 13 months ago by
ATpoint
★ 3.9k • written 13 months ago by
Tyroone
• 0
0
votes
1
reply
442
views
Analysis with Batch correction
DESeq2
BatchEffect
updated 13 months ago by
Michael Love
41k • written 13 months ago by
giulia.lopatriello
• 0
1
vote
1
reply
688
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR
model.matrix
BatchEffect
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
greta
• 0
5
votes
2
replies
718
views
Sva and batch effect
limma
BatchEffect
sva
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
Lenny186
• 0
1
vote
1
reply
1.4k
views
batch effect correction before DESeq2 analysis
DESeq2
BatchEffect
updated 13 months ago by
ATpoint
★ 3.9k • written 13 months ago by
luca.s
▴ 50
0
votes
0
replies
640
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
14 months ago
Zhijie
• 0
1
vote
0
replies
575
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran
Normalization
scRNA
BatchEffect
14 months ago
r_grau
▴ 10
1
vote
2
replies
814
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2
BatchEffect
RNASeq
updated 17 months ago by
swbarnes2
★ 1.3k • written 17 months ago by
Flavio
• 0
3
votes
10
replies
1.8k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2
BatchEffect
fold
17 months ago
eve.olszanowski
• 0
1
vote
2
replies
744
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2
BatchEffect
17 months ago
annamariabugaj
▴ 10
0
votes
1
reply
897
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 19 months ago by
Michael Love
41k • written 19 months ago by
estafana.t98
• 0
0
votes
1
reply
827
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData
BatchEffect
r
limma
updated 19 months ago by
Gordon Smyth
50k • written 19 months ago by
mfaleevs
• 0
1
vote
1
reply
664
views
RNA-Seq normalization and batch effect removal
RNASeq
BatchEffect
DESeq2
updated 21 months ago by
Michael Love
41k • written 21 months ago by
Alexandre
• 0
6
votes
7
replies
1.7k
views
Batch effect with one sample being in two batches
BatchEffect
DESeq2
21 months ago
lmrogers34
▴ 10
2
votes
1
reply
1.2k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma
BatchEffect
updated 21 months ago by
Gordon Smyth
50k • written 21 months ago by
nhaus
▴ 10
0
votes
1
reply
843
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 23 months ago by
Gordon Smyth
50k • written 23 months ago by
Mageiros
• 0
1
vote
1
reply
982
views
How to determine if limma can adjust for batch effect
BatchEffect
limma
sva
DifferentialExpression
updated 2.1 years ago by
ATpoint
★ 3.9k • written 2.1 years ago by
nhaus
▴ 10
0
votes
0
replies
479
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
2.1 years ago
Ety
• 0
1
vote
7
replies
1.2k
views
Comparison DESeq results using different model
Batch
BatchEffect
DESeq2
updated 2.1 years ago by
James W. MacDonald
65k • written 2.1 years ago by
dequattro.concetta
▴ 10
0
votes
2
replies
991
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch
RNASeq
BatchEffect
DESeq2
updated 2.2 years ago by
Steve Lianoglou
★ 13k • written 2.2 years ago by
Jonas
• 0
0
votes
2
replies
874
views
Design formula in DESeq2
model
BatchEffect
hidden
Design
DESeq2
2.4 years ago
m.glymenaki
• 0
6
votes
6
replies
1.3k
views
Batch effect from to sequencing data at differents depths
Sequencing
sequencingDeepth
BatchEffect
DESeq2
2.4 years ago
ary.lech
▴ 10
50 results • Page
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Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
Efra
• 0
I did as you told, and after running ```eset.annot <- annotateEset(eset, hugene11sttranscriptcluster.db)``` I got the next output: ``` 'se…
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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