Showing : SVAseq • reset
2
votes
2
replies
556
views
Double normalising when using sva and deseq2
DESeq2 Normalisation Bulkrnaseq Svaseq
8 months ago BioinfGuru ▴ 70
0
votes
1
reply
873
views
how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
2.6 years ago Tongjun • 0
0
votes
0
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1.3k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
votes
0
replies
1.0k
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
3.4 years ago georgia.katsoula ▴ 40
0
votes
1
reply
989
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 4.8 years ago by 68k • written 4.8 years ago by ▴ 30
1
vote
1
reply
1.1k
views
svaseq - over adjustment
svaseq sva
5.9 years ago flippy23 • 0
1
vote
1
reply
1.0k
views
sva correction for MEDIPS
MEDIPS svaseq sva
updated 6.0 years ago by ▴ 570 • written 6.0 years ago by • 0
2
votes
3
replies
2.0k
views
Batch-effect: batch in design and corrected batch with sva- DESeq2
deseq2 svaseq
6.0 years ago bioinfo • 0
3
votes
4
replies
1.8k
views
Calling svaseq() multiple times
edger sva svaseq limma
updated 6.7 years ago by ★ 7.9k • written 6.7 years ago by ▴ 20
1
vote
2
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3.7k
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Applying SVA to RNA-Seq dataset
DESeq2 sva svaseq batch effect correction
7.0 years ago L_K • 0
0
votes
0
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1.3k
views
correlated known batch effect correction using svaseq
svaseq batcheffectcorrection
7.2 years ago burcu.atasu • 0
1
vote
1
reply
1.7k
views
Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 7.3 years ago by ▴ 980 • written 7.3 years ago by ▴ 10
0
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0
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1.4k
views
Batch correction with uncertain biological variables
sva svaseq batch effect batch effects batch effect correction
7.5 years ago vedran.franke • 0
1
vote
6
replies
1.9k
views
RNASeq fold change analysis after subtraction of contaminating MEF signal
deseq2 svaseq
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 10
3
votes
4
replies
2.1k
views
Taking surrogate variable into account before running PCA
sva svaseq
updated 7.6 years ago by ★ 4.1k • written 7.6 years ago by • 0
3
votes
2
replies
2.7k
views
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
limma sva svaseq
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 670
2
votes
7
replies
2.0k
views
Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
svaseq dexseq
updated 8.0 years ago by ★ 1.9k • written 8.0 years ago by • 0
3
votes
6
replies
2.9k
views
is it necessary to check batch effect in this case? and how to?
svaseq combat sva RANseq batcheffect removebatcheffect
updated 8.3 years ago by ▴ 50 • written 8.3 years ago by ▴ 10
5
votes
7
replies
5.9k
views
Correcting for known and surrogate variables in DESeq2
deseq2 svaseq
8.3 years ago Akula, Nirmala NIH/NIMH [C] ▴ 190
2
votes
1
reply
2.1k
views
Regarding batch effect in Deseq2 package
deseq2 sva svaseq
updated 8.5 years ago by 43k • written 8.5 years ago by ▴ 20
0
votes
3
replies
2.8k
views
can we use sva function to estimate artifacts for rna seq data?
sva svaseq batcheffectcorrection
updated 8.5 years ago by ▴ 650 • written 8.5 years ago by ▴ 20
1
vote
5
replies
4.1k
views
PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2 sva svaseq pca
8.7 years ago Peter Alto ▴ 10
22 results • Page 1 of 1
Recent ...
Replies
Comment: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = by SofieK • 0
Thank you, I will try this and see.
Comment: DiffBind - question on the use of filtered or unfiltered input data by deltaexploitss • 0
Data input is the adding of data into a computer. This can take place through an input device such as a keyboard. A user inputs data, which…
Comment: GenomeInfoDbData cannot install in R and warning had non-zero exit status by Renuka • 0
how you did it pls explain
Answer: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = by James W. MacDonald 68k
If I understand correctly, you want to assess differential transcript abundances. If so, there are a couple of ways you can do that. One wa…
Answer: Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes by a.alkema • 0
Oh, that's silly - thanks, will do!
Votes
A: Effect of lfcThreshold on p-value in DESeq2
Answer: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
Answer: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode =
Comment: Unused arguments error without used arguments in GSVA?
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