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SVAseq
•
reset
0
votes
1
reply
607
views
how to identify the unwanted variables independent of phenotypes
RUVSeq
svaseq
21 months ago
Tongjun
• 0
0
votes
0
replies
1.1k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 2.2 years ago by
James W. MacDonald
65k • written 2.2 years ago by
Bex
• 0
0
votes
0
replies
772
views
SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
2.6 years ago
georgia.katsoula
▴ 40
0
votes
1
reply
752
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
1
vote
1
reply
911
views
svaseq - over adjustment
svaseq
sva
5.1 years ago
flippy23
• 0
1
vote
1
reply
867
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
2
votes
3
replies
1.5k
views
Batch-effect: batch in design and corrected batch with sva- DESeq2
deseq2
svaseq
5.2 years ago
bioinfo
• 0
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
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
0
replies
1.1k
views
correlated known batch effect correction using svaseq
svaseq
batcheffectcorrection
6.4 years ago
burcu.atasu
• 0
1
vote
1
reply
1.5k
views
Outputting batch-effect free normalized counts
ruvseq
svaseq
edaseq
updated 6.4 years ago by
davide risso
▴ 950 • written 6.5 years ago by
llo
▴ 10
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
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
3
votes
4
replies
1.7k
views
Taking surrogate variable into account before running PCA
sva
svaseq
updated 6.8 years ago by
Guido Hooiveld
★ 3.9k • written 6.8 years ago by
wamiqsaifi
• 0
3
votes
2
replies
2.5k
views
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
limma
sva
svaseq
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
Bogdan
▴ 670
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
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
5
votes
7
replies
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
1
reply
1.6k
views
Regarding batch effect in Deseq2 package
deseq2
sva
svaseq
updated 7.6 years ago by
Michael Love
41k • written 7.7 years ago by
szenitha
▴ 20
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
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 • updated 7.8 years ago
Peter Alto
▴ 10
21 results • Page
1 of 1
Recent ...
Replies
Comment: Which input file is used for DGEList in EgdeR?
by
i.atanasoai
• 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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