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svaseq
•
reset
5
votes
7
replies
5.1k
views
Correcting for known and surrogate variables in DESeq2
deseq2
svaseq
7.6 years ago
Akula, Nirmala NIH/NIMH [C]
▴ 190
2
votes
7
replies
1.8k
views
Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
svaseq
dexseq
updated 7.2 years ago by
Alejandro Reyes
★ 1.9k • written 7.2 years ago by
tofukaj
• 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
Jakub
▴ 50 • written 7.5 years ago by
amoltej
▴ 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
Michael Love
41k • written 6.7 years ago by
gpalidwor
▴ 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
replies
1.4k
views
Calling svaseq() multiple times
edger
sva
svaseq
limma
updated 5.9 years ago by
Ryan C. Thompson
★ 7.9k • written 5.9 years ago by
cats_dogs
▴ 20
3
votes
4
replies
1.7k
views
Taking surrogate variable into account before running PCA
sva
svaseq
updated 6.9 years ago by
Guido Hooiveld
★ 3.9k • written 6.9 years ago by
wamiqsaifi
• 0
2
votes
3
replies
1.5k
views
Batch-effect: batch in design and corrected batch with sva- DESeq2
deseq2
svaseq
5.3 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
Jeff Leek
▴ 650 • written 7.7 years ago by
szenitha
▴ 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
Aaron Lun
★ 28k • written 7.2 years ago by
Bogdan
▴ 670
1
vote
2
replies
3.1k
views
Applying SVA to RNA-Seq dataset
DESeq2
sva
svaseq
batch effect correction
6.3 years ago
L_K
• 0
0
votes
1
reply
614
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
davide risso
▴ 950 • written 6.5 years ago by
llo
▴ 10
2
votes
1
reply
1.6k
views
Regarding batch effect in Deseq2 package
deseq2
sva
svaseq
updated 7.7 years ago by
Michael Love
41k • written 7.7 years ago by
szenitha
▴ 20
1
vote
1
reply
869
views
sva correction for MEDIPS
MEDIPS
svaseq
sva
updated 5.2 years ago by
Lukas Chavez
▴ 570 • written 5.2 years ago by
tofukaj
• 0
1
vote
1
reply
916
views
svaseq - over adjustment
svaseq
sva
5.1 years ago
flippy23
• 0
0
votes
1
reply
756
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
Mozart
▴ 30
0
votes
0
replies
1.1k
views
correlated known batch effect correction using svaseq
svaseq
batcheffectcorrection
6.5 years ago
burcu.atasu
• 0
0
votes
0
replies
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
replies
1.1k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 2.3 years ago by
James W. MacDonald
65k • written 2.3 years ago by
Bex
• 0
0
votes
0
replies
779
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
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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