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svaseq
•
reset
0
votes
1
reply
476
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
17 months ago
Tongjun
• 0
0
votes
0
replies
927
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 23 months ago by
James W. MacDonald
64k • written 23 months ago by
Bex
• 0
0
votes
0
replies
666
views
SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
2.2 years ago
georgia.katsoula
▴ 40
0
votes
1
reply
647
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 3.7 years ago by
James W. MacDonald
64k • written 3.7 years ago by
Mozart
▴ 30
1
vote
1
reply
811
views
svaseq - over adjustment
svaseq
sva
4.7 years ago
flippy23
• 0
1
vote
1
reply
771
views
sva correction for MEDIPS
MEDIPS
svaseq
sva
updated 4.9 years ago by
Lukas Chavez
▴ 570 • written 4.9 years ago by
tofukaj
• 0
2
votes
3
replies
1.3k
views
Batch-effect: batch in design and corrected batch with sva- DESeq2
deseq2
svaseq
4.9 years ago
bioinfo
• 0
3
votes
4
replies
1.3k
views
Calling svaseq() multiple times
edger
sva
svaseq
limma
updated 5.6 years ago by
Ryan C. Thompson
7.8k • written 5.6 years ago by
cats_dogs
▴ 20
1
vote
2
replies
2.9k
views
Applying SVA to RNA-Seq dataset
DESeq2
sva
svaseq
batch effect correction
5.9 years ago
L_K
• 0
0
votes
0
replies
931
views
correlated known batch effect correction using svaseq
svaseq
batcheffectcorrection
6.1 years ago
burcu.atasu
• 0
1
vote
1
reply
1.3k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 6.1 years ago by
davide risso
▴ 930 • written 6.1 years ago by
llo
▴ 10
0
votes
0
replies
1.1k
views
Batch correction with uncertain biological variables
sva
svaseq
batch effect
batch effects
batch effect correction
6.3 years ago
vedran.franke
• 0
1
vote
6
replies
1.6k
views
RNASeq fold change analysis after subtraction of contaminating MEF signal
deseq2
svaseq
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
gpalidwor
▴ 10
3
votes
4
replies
1.5k
views
Taking surrogate variable into account before running PCA
sva
svaseq
updated 6.5 years ago by
Guido Hooiveld
★ 3.8k • written 6.5 years ago by
wamiqsaifi
• 0
3
votes
2
replies
2.4k
views
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
limma
sva
svaseq
updated 6.8 years ago by
Aaron Lun
★ 28k • written 6.8 years ago by
Bogdan
▴ 670
2
votes
7
replies
1.6k
views
Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
svaseq
dexseq
updated 6.8 years ago by
Alejandro Reyes
★ 1.9k • written 6.8 years ago by
tofukaj
• 0
3
votes
6
replies
2.0k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 7.1 years ago by
Jakub
▴ 50 • written 7.1 years ago by
amoltej
▴ 10
5
votes
7
replies
4.7k
views
Correcting for known and surrogate variables in DESeq2
deseq2
svaseq
7.2 years ago
Akula, Nirmala NIH/NIMH [C]
▴ 190
2
votes
1
reply
1.5k
views
Regarding batch effect in Deseq2 package
deseq2
sva
svaseq
updated 7.3 years ago by
Michael Love
41k • written 7.3 years ago by
szenitha
▴ 20
0
votes
3
replies
2.2k
views
can we use sva function to estimate artifacts for rna seq data?
sva
svaseq
batcheffectcorrection
updated 7.3 years ago by
Jeff Leek
▴ 640 • written 7.3 years ago by
szenitha
▴ 20
1
vote
5
replies
3.4k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2
sva
svaseq
pca
7.5 years ago
Peter Alto
▴ 10
21 results • Page
1 of 1
Recent ...
Replies
Answer: Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DE
by
James W. MacDonald
64k
The short answer is that you don't. `tximport` is meant to summarize transcript abundance estimates at the gene level, and as you might ima…
Comment: Inconsistent results in DiffBind
by
ATpoint
★ 3.6k
One is the "raw" logFCs, not corrected for the standard error of the logFCs, the other one the shrunken logFCs from DESeq2 lfcShrink, "corr…
Answer: Can't download Bioconductor
by
James W. MacDonald
64k
[You need to update][1]. [1]: https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html#basic-use
Comment: Can't download Bioconductor
by
ATpoint
★ 3.6k
Please see especially the 1st and 2nd point in https://www.bioconductor.org/help/support/posting-guide/#keypoints
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
by
Michael Love
41k
With 3 vs 3, when one sample increases from 50 to 5000, this can lead to rejection of null hypothesis. I'm not surprised with the above cou…
Votes
Answer: biomaRt not working - lazy table error
Answer: Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DE
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
Answer: What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)
Answer: WGCNA documentation not available
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