Showing : SVA • reset
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2.0k
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SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 9 weeks ago by • 0 • written 4.2 years ago by ▴ 10
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1
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147
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 9 weeks ago by ▴ 50 • written 9 weeks ago by • 0
0
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2
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242
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How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
4 months ago Xiaojie Cheng • 0
0
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3
replies
222
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ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 4 months ago by 3.2k • written 4 months ago by • 0
0
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1
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133
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How to set mod0 in sva analysis
sva
updated 5 months ago by ★ 2.7k • written 5 months ago by • 0
2
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2
replies
186
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Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 5 months ago by ▴ 700 • written 5 months ago by • 0
1
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8
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340
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Error in running Combat function
sva ComBat
updated 6 months ago by 3.2k • written 6 months ago by ▴ 10
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0
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236
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
6 months ago Papyrus ▴ 10
0
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5
replies
189
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Variable of interest in combat correction
sva combat
updated 8 months ago by 57k • written 8 months ago by ▴ 10
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3
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217
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Extracting a subset of samples following SVA
Combat SVA Limma
updated 10 months ago by 3.2k • written 10 months ago by • 0
0
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10
replies
242
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Running SVA changes format of time variable in model
sva proxitct hms
updated 10 months ago by 57k • written 10 months ago by • 0
7
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6
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263
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sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 14 months ago by ▴ 840 • written 15 months ago by ▴ 10
0
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1
reply
127
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 15 months ago by 57k • written 15 months ago by ▴ 20
0
votes
1
reply
135
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 16 months ago by 57k • written 16 months ago by • 0
1
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1
reply
143
views
SVA paired samples
SVA EPIC methylation limma
updated 17 months ago by 57k • written 17 months ago by • 0
2
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4
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203
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DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 17 months ago by 33k • written 17 months ago by • 0
1
vote
2
replies
180
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 18 months ago by 43k • written 18 months ago by • 0
0
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0
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434
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adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
19 months ago anne.bozack • 0
0
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1
reply
219
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 20 months ago by ▴ 840 • written 20 months ago by ▴ 10
0
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0
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182
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limma-voom group design and its effect on sva
limma voom group-design sva
20 months ago kentfung • 0
0
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8
replies
277
views
Error in sva() function: missing values, NaNs produced
sva batch-correction
updated 21 months ago by 57k • written 21 months ago by ▴ 10
0
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3
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250
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 21 months ago by 25k • written 21 months ago by • 0
2
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5
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385
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 22 months ago by ★ 2.7k • written 22 months ago by • 0
0
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1
reply
268
views
Handling adjustment variables and surrogate variables in model
sva deseq2
updated 22 months ago by 57k • written 22 months ago by • 0
1
vote
1
reply
263
views
Bioconductor SVA: two variables of interest
sva
updated 22 months ago by 57k • written 22 months ago by • 0
4
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5
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301
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 23 months ago by • 0 • written 23 months ago by • 0
0
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2
replies
230
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 23 months ago by 33k • written 23 months ago by • 0
0
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3
replies
240
views
Design matrix for cohort with samples outside "block"
limma voom sva
23 months ago kentfung • 0
0
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0
replies
173
views
fsva function does not work without newdat argument
sva
23 months ago jakob.wirbel • 0
0
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0
replies
257
views
The correct specification of the model matrix to ComBat
ComBat sva
23 months ago Sam ▴ 10
7
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4
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1.5k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 2.0 years ago by 43k • written 2.0 years ago by ▴ 620
0
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0
replies
294
views
Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
2.1 years ago kentfung • 0
0
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1
reply
328
views
Using surrogate variables as covariates in WGBS differential methylation calling
dmrseq sva DSS
updated 2.1 years ago by ▴ 60 • written 2.1 years ago by • 0
1
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8
replies
775
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 2.1 years ago by 33k • written 2.1 years ago by • 0
2
votes
1
reply
445
views
Using SVA (surrogate variable analysis) to correct for 'completely' confounded cell type composition in DNA methylation data
sva linear model cell type composition R microarray
2.2 years ago Papyrus ▴ 10
5
votes
3
replies
589
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna coexpression sva
updated 2.2 years ago by ★ 2.6k • written 2.2 years ago by ▴ 230
0
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1
reply
266
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 2.2 years ago by 33k • written 2.2 years ago by ▴ 20
3
votes
12
replies
1.1k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 2.3 years ago by 57k • written 2.3 years ago by ▴ 10
1
vote
1
reply
310
views
svaseq - over adjustment
svaseq sva
2.3 years ago flippy23 • 0
0
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8
replies
443
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 2.3 years ago by 33k • written 2.3 years ago by • 0
1
vote
2
replies
496
views
Normalized transcript/exon counts for network analysis
drimseq dexseq wgcna sva
updated 2.4 years ago by ▴ 80 • written 2.4 years ago by ▴ 20
4
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4
replies
654
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 570
0
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0
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478
views
OpenBLAS issue with ComBat() function of the R SVA package on Torque cluster
sva R OpenBLAS
updated 2.5 years ago by 57k • written 2.5 years ago by • 0
4
votes
2
replies
4.0k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 2.5 years ago by • 0 • written 3.8 years ago by ▴ 60
1
vote
1
reply
356
views
sva correction for MEDIPS
MEDIPS svaseq sva
updated 2.5 years ago by ▴ 550 • written 2.5 years ago by • 0
0
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7
replies
552
views
paired sample - SVA model matrix
limma sva paired sample
updated 2.6 years ago by 57k • written 2.6 years ago by • 0
1
vote
1
reply
520
views
Define batch effect variables before removing them or getting rid of hidden surrogate variables
batch effect correction sva proteomics
2.7 years ago Sebastian Hesse ▴ 50
1
vote
10
replies
2.2k
views
SVAseq and DESeq2 workflow
sva deseq2
updated 2.8 years ago by 33k • written 2.8 years ago by • 0
0
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0
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293
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Sva for tumor cellular heterogeneity
limma sva
2.8 years ago chp950 • 0
0
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2
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608
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 2.9 years ago by 33k • written 2.9 years ago by • 0
50 results • Page 1 of 1
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Comment: Best practice for quantifying sncRNA by Abhishek • 0
k has to be odd - trying 9, 21 instead
Comment: Best practice for quantifying sncRNA by Abhishek • 0
I did use the genome as decoy. And I used whole transcriptome from Gencode for indexing. Maybe I should index using just non coding transc…
Comment: Best practice for quantifying sncRNA by Abhishek • 0
Thank you for your suggestions. Throwing away larger reads sounds true, I'll try using Cutadapt for that besides adapter trimming. I did …
Comment: Best practice for quantifying sncRNA by Abhishek • 0
Thanks, I will try out Bowtie. Is GeneGlobe and Qiagen the same company ? https://www.qiagen.com/us/resources/download.aspx?id=bea2dcfa-…
Answer: Using both spike in and TMM normalizations in ChIP-seq samples by Gordon Smyth 43k
It is impossible to use both spike-in or TMM normalization. You must do one or the other. They replace each other, they cannot be combined.…
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Comment: Idea: Using DESeq2 to test a change in ratio of two genes
Time Series Analysis
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Answer: Time series DE gene analysis with edgeR where specific timepoints have NA levels
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