Showing : Svaseq • reset
2
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2
replies
662
views
Double normalising when using sva and deseq2
DESeq2 Normalisation Bulkrnaseq Svaseq
9 months ago BioinfGuru ▴ 70
0
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1
reply
921
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how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
2.7 years ago Tongjun • 0
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0
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1.4k
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SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
0
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0
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1.1k
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SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
3.5 years ago georgia.katsoula ▴ 40
0
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1
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1.0k
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SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 30
1
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1
reply
1.1k
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svaseq - over adjustment
svaseq sva
6.0 years ago flippy23 • 0
1
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1
reply
1.1k
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sva correction for MEDIPS
MEDIPS svaseq sva
updated 6.2 years ago by ▴ 570 • written 6.2 years ago by • 0
2
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3
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2.1k
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Batch-effect: batch in design and corrected batch with sva- DESeq2
deseq2 svaseq
6.2 years ago bioinfo • 0
3
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4
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1.9k
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Calling svaseq() multiple times
edger sva svaseq limma
updated 6.9 years ago by ★ 7.9k • written 6.9 years ago by ▴ 20
1
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2
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3.9k
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Applying SVA to RNA-Seq dataset
DESeq2 sva svaseq batch effect correction
7.2 years ago L_K • 0
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0
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1.3k
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correlated known batch effect correction using svaseq
svaseq batcheffectcorrection
7.4 years ago burcu.atasu • 0
1
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1
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1.8k
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Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 7.4 years ago by ▴ 980 • written 7.4 years ago by ▴ 10
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0
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1.5k
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Batch correction with uncertain biological variables
sva svaseq batch effect batch effects batch effect correction
7.6 years ago vedran.franke • 0
1
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6
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2.0k
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RNASeq fold change analysis after subtraction of contaminating MEF signal
deseq2 svaseq
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 10
3
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4
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2.1k
views
Taking surrogate variable into account before running PCA
sva svaseq
updated 7.8 years ago by ★ 4.1k • written 7.8 years ago by • 0
3
votes
2
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2.8k
views
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
limma sva svaseq
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 670
2
votes
7
replies
2.1k
views
Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
svaseq dexseq
updated 8.2 years ago by ★ 1.9k • written 8.2 years ago by • 0
3
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6
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3.0k
views
is it necessary to check batch effect in this case? and how to?
svaseq combat sva RANseq batcheffect removebatcheffect
updated 8.5 years ago by ▴ 50 • written 8.5 years ago by ▴ 10
5
votes
7
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6.1k
views
Correcting for known and surrogate variables in DESeq2
deseq2 svaseq
8.5 years ago Akula, Nirmala NIH/NIMH [C] ▴ 190
2
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1
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2.1k
views
Regarding batch effect in Deseq2 package
deseq2 sva svaseq
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 20
0
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3
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2.9k
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can we use sva function to estimate artifacts for rna seq data?
sva svaseq batcheffectcorrection
updated 8.7 years ago by ▴ 650 • written 8.7 years ago by ▴ 20
1
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5
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4.1k
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PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2 sva svaseq pca
8.8 years ago Peter Alto ▴ 20
22 results • Page 1 of 1
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Replies
Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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