Showing : svaseq • reset
5
votes
7
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5.1k
views
Correcting for known and surrogate variables in DESeq2
deseq2 svaseq
7.5 years ago Akula, Nirmala NIH/NIMH [C] ▴ 190
2
votes
7
replies
1.7k
views
Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
svaseq dexseq
updated 7.2 years ago by ★ 1.9k • written 7.2 years ago by • 0
3
votes
6
replies
2.2k
views
is it necessary to check batch effect in this case? and how to?
svaseq combat sva RANseq batcheffect removebatcheffect
updated 7.5 years ago by ▴ 50 • written 7.5 years ago by ▴ 10
1
vote
6
replies
1.7k
views
RNASeq fold change analysis after subtraction of contaminating MEF signal
deseq2 svaseq
updated 6.7 years ago by 41k • written 6.7 years ago by ▴ 10
1
vote
5
replies
3.7k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2 sva svaseq pca
7.9 years ago Peter Alto ▴ 10
3
votes
4
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1.4k
views
Calling svaseq() multiple times
edger sva svaseq limma
updated 5.9 years ago by ★ 7.9k • written 5.9 years ago by ▴ 20
3
votes
4
replies
1.7k
views
Taking surrogate variable into account before running PCA
sva svaseq
updated 6.8 years ago by ★ 3.9k • written 6.8 years ago by • 0
2
votes
3
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1.5k
views
Batch-effect: batch in design and corrected batch with sva- DESeq2
deseq2 svaseq
5.2 years ago bioinfo • 0
0
votes
3
replies
2.4k
views
can we use sva function to estimate artifacts for rna seq data?
sva svaseq batcheffectcorrection
updated 7.7 years ago by ▴ 650 • written 7.7 years ago by ▴ 20
3
votes
2
replies
2.5k
views
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
limma sva svaseq
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 670
1
vote
2
replies
3.1k
views
Applying SVA to RNA-Seq dataset
DESeq2 sva svaseq batch effect correction
6.2 years ago L_K • 0
0
votes
1
reply
607
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
21 months ago Tongjun • 0
1
vote
1
reply
1.5k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 6.5 years ago by ▴ 950 • written 6.5 years ago by ▴ 10
2
votes
1
reply
1.6k
views
Regarding batch effect in Deseq2 package
deseq2 sva svaseq
updated 7.7 years ago by 41k • written 7.7 years ago by ▴ 20
1
vote
1
reply
867
views
sva correction for MEDIPS
MEDIPS svaseq sva
updated 5.2 years ago by ▴ 570 • written 5.2 years ago by • 0
1
vote
1
reply
911
views
svaseq - over adjustment
svaseq sva
5.1 years ago flippy23 • 0
0
votes
1
reply
752
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 4.0 years ago by 65k • written 4.0 years ago by ▴ 30
0
votes
0
replies
1.1k
views
correlated known batch effect correction using svaseq
svaseq batcheffectcorrection
6.4 years ago burcu.atasu • 0
0
votes
0
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1.2k
views
Batch correction with uncertain biological variables
sva svaseq batch effect batch effects batch effect correction
6.7 years ago vedran.franke • 0
0
votes
0
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1.1k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 2.3 years ago by 65k • written 2.3 years ago by • 0
0
votes
0
replies
773
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
2.6 years ago georgia.katsoula ▴ 40
21 results • Page 1 of 1
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Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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