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batcheffect
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150
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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
352
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
516
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
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
29 results • Page
1 of 1
Recent ...
Replies
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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Gordon Smyth
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James W. MacDonald
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