Showing : Svaseq • reset
2
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2
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856
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Double normalising when using sva and deseq2
DESeq2 Normalisation Bulkrnaseq Svaseq
16 months ago BioinfGuru ▴ 70
0
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1
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1.0k
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how to identify the unwanted variables independent of phenotypes
RUVSeq svaseq
3.2 years ago Tongjun • 0
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0
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1.5k
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SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
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0
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1.2k
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SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
4.0 years ago georgia.katsoula ▴ 40
0
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1
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1.1k
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SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 30
1
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1
reply
1.3k
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svaseq - over adjustment
svaseq sva
6.5 years ago flippy23 • 0
1
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1
reply
1.2k
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sva correction for MEDIPS
MEDIPS svaseq sva
updated 6.7 years ago by ▴ 570 • written 6.7 years ago by • 0
2
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3
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2.3k
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Batch-effect: batch in design and corrected batch with sva- DESeq2
deseq2 svaseq
6.7 years ago bioinfo • 0
3
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4
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2.1k
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Calling svaseq() multiple times
edger sva svaseq limma
updated 7.4 years ago by ★ 7.9k • written 7.4 years ago by ▴ 20
1
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2
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4.1k
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Applying SVA to RNA-Seq dataset
DESeq2 sva svaseq batch effect correction
7.7 years ago L_K • 0
0
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0
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1.4k
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correlated known batch effect correction using svaseq
svaseq batcheffectcorrection
7.9 years ago burcu.atasu • 0
1
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1
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2.0k
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Outputting batch-effect free normalized counts
ruvseq svaseq edaseq
updated 7.9 years ago by ▴ 980 • written 7.9 years ago by ▴ 10
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0
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1.6k
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Batch correction with uncertain biological variables
sva svaseq batch effect batch effects batch effect correction
8.2 years ago vedran.franke • 0
1
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6
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2.2k
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RNASeq fold change analysis after subtraction of contaminating MEF signal
deseq2 svaseq
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
3
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4
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2.3k
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Taking surrogate variable into account before running PCA
sva svaseq
updated 8.3 years ago by ★ 4.1k • written 8.3 years ago by • 0
3
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2
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2.9k
views
(batch) corrections of RNA-seq data: integrating LIMMA and SVA
limma sva svaseq
updated 8.6 years ago by ★ 29k • written 8.6 years ago by ▴ 670
2
votes
7
replies
2.2k
views
Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
svaseq dexseq
updated 8.7 years ago by ★ 1.9k • written 8.7 years ago by • 0
3
votes
6
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3.3k
views
is it necessary to check batch effect in this case? and how to?
svaseq combat sva RANseq batcheffect removebatcheffect
updated 9.0 years ago by ▴ 50 • written 9.0 years ago by ▴ 10
5
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7
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6.4k
views
Correcting for known and surrogate variables in DESeq2
deseq2 svaseq
9.0 years ago Akula, Nirmala NIH/NIMH [C] ▴ 190
2
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1
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2.3k
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Regarding batch effect in Deseq2 package
deseq2 sva svaseq
updated 9.1 years ago by 43k • written 9.1 years ago by ▴ 20
0
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3
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3.1k
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can we use sva function to estimate artifacts for rna seq data?
sva svaseq batcheffectcorrection
updated 9.2 years ago by ▴ 650 • written 9.2 years ago by ▴ 20
1
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5
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4.3k
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PCA of svaseq "cleaned" counts and DESeq2 SV subtracted counts are different?
deseq2 sva svaseq pca
9.3 years ago Peter Alto ▴ 20
22 results • Page 1 of 1
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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