Showing : SVA • reset
1
vote
1
reply
58
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
3 days ago • updated 2 days ago takemoto • 0
0
votes
1
reply
92
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 5 weeks ago by 45k • written 5 weeks ago by • 0
1
vote
1
reply
176
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 12 weeks ago by ★ 1.2k • written 12 weeks ago by • 0
1
vote
4
replies
330
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
3 months ago • updated 12 weeks ago Clay • 0
0
votes
0
replies
228
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 4 months ago by 59k • written 4 months ago by • 0
0
votes
5
replies
1.0k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 4 months ago by ★ 1.2k • written 14 months ago by • 0
0
votes
0
replies
238
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
7 months ago georgia.katsoula ▴ 40
0
votes
4
replies
1.1k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
8 months ago NewBioInfo • 0
1
vote
2
replies
344
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
9 months ago Ahdee ▴ 50
0
votes
1
reply
2.4k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 12 months ago by • 0 • written 5.1 years ago by ▴ 10
0
votes
1
reply
507
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 12 months ago by ▴ 50 • written 12 months ago by • 0
1
vote
3
replies
428
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 14 months ago by 3.5k • written 14 months ago by • 0
0
votes
1
reply
413
views
How to set mod0 in sva analysis
sva
updated 15 months ago by ★ 2.8k • written 15 months ago by • 0
2
votes
2
replies
362
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 15 months ago by ★ 1.2k • written 15 months ago by • 0
0
votes
0
replies
414
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
16 months ago epibio ▴ 10
1
vote
8
replies
548
views
Error in running Combat function
sva ComBat
updated 16 months ago by 3.5k • written 16 months ago by ▴ 10
0
votes
5
replies
400
views
Variable of interest in combat correction
sva combat
updated 18 months ago by 59k • written 18 months ago by ▴ 10
0
votes
3
replies
362
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 19 months ago by 3.5k • written 20 months ago by • 0
0
votes
10
replies
466
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 20 months ago by 59k • written 20 months ago by • 0
7
votes
6
replies
497
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 2.0 years ago by ▴ 840 • written 2.0 years ago by ▴ 10
0
votes
1
reply
249
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 2.1 years ago by 59k • written 2.1 years ago by ▴ 20
0
votes
1
reply
240
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 2.2 years ago by 59k • written 2.2 years ago by • 0
1
vote
1
reply
320
views
SVA paired samples
SVA EPIC methylation limma
updated 2.2 years ago by 59k • written 2.2 years ago by • 0
2
votes
4
replies
399
views
DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 2.3 years ago by 37k • written 2.3 years ago by • 0
1
vote
2
replies
338
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 2.3 years ago by 45k • written 2.3 years ago by • 0
0
votes
0
replies
811
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
2.4 years ago anne.bozack • 0
0
votes
1
reply
362
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 2.5 years ago by ▴ 840 • written 2.5 years ago by ▴ 10
0
votes
0
replies
326
views
limma-voom group design and its effect on sva
limma voom group-design sva
2.5 years ago kentfung • 0
0
votes
8
replies
493
views
Error in sva() function: missing values, NaNs produced
sva batch-correction
updated 2.5 years ago by 59k • written 2.5 years ago by ▴ 10
0
votes
3
replies
419
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 2.6 years ago by 25k • written 2.6 years ago by • 0
2
votes
5
replies
573
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 2.6 years ago by ★ 2.8k • written 2.7 years ago by • 0
0
votes
1
reply
445
views
Handling adjustment variables and surrogate variables in model
sva deseq2
updated 2.7 years ago by 59k • written 2.7 years ago by • 0
1
vote
1
reply
459
views
Bioconductor SVA: two variables of interest
sva
updated 2.7 years ago by 59k • written 2.7 years ago by • 0
4
votes
5
replies
416
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 2.7 years ago by • 0 • written 2.7 years ago by • 0
0
votes
2
replies
387
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 2.7 years ago by 37k • written 2.7 years ago by • 0
0
votes
3
replies
352
views
Design matrix for cohort with samples outside "block"
limma voom sva
2.8 years ago kentfung • 0
0
votes
0
replies
260
views
fsva function does not work without newdat argument
sva
2.8 years ago jakob.wirbel • 0
0
votes
0
replies
345
views
The correct specification of the model matrix to ComBat
ComBat sva
2.8 years ago Sam ▴ 10
7
votes
4
replies
2.4k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 2.8 years ago by 45k • written 2.8 years ago by ▴ 640
0
votes
0
replies
471
views
Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
2.9 years ago kentfung • 0
0
votes
1
reply
525
views
Using surrogate variables as covariates in WGBS differential methylation calling
dmrseq sva DSS
updated 2.9 years ago by ▴ 60 • written 2.9 years ago by • 0
2
votes
8
replies
1.2k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 2.9 years ago by 37k • written 2.9 years ago by ▴ 10
2
votes
1
reply
743
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
3.0 years ago epibio ▴ 10
5
votes
3
replies
945
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna coexpression sva
updated 3.0 years ago by ★ 2.6k • written 3.0 years ago by ▴ 240
0
votes
1
reply
388
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 3.1 years ago by 37k • written 3.1 years ago by ▴ 20
3
votes
12
replies
1.5k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 3.1 years ago by 59k • written 3.1 years ago by ▴ 10
1
vote
1
reply
446
views
svaseq - over adjustment
svaseq sva
3.2 years ago flippy23 • 0
0
votes
8
replies
641
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 3.2 years ago by 37k • written 3.2 years ago by • 0
1
vote
2
replies
670
views
Normalized transcript/exon counts for network analysis
drimseq dexseq wgcna sva
updated 3.2 years ago by ▴ 90 • written 3.3 years ago by ▴ 20
4
votes
4
replies
899
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 3.3 years ago by 45k • written 3.3 years ago by ▴ 610
50 results • Page 1 of 1
Recent ...
Replies
Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
Ok.. thanks for your valuable suggestion and quick replies. I have generated an MA plot using plotMASwish. thanks ekta
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by Michael Love 37k
Sorry, I haven't seen this. Maybe try filtering low count genes? ``` keep <- rowSums(counts(dds) >= 10) >= X dds <- dds[keep,] # then run …
Comment: Transcript-level differential expression using DESeq2 by Michael Love 37k
To show some extent of the DTE you can plot the LFC of the significant set and their mean count, we have `plotMASwish` to do this. Another…
Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
No, the Volcano plot is not essential. I just wanted to show DETs with the help of a plot. Could you suggest a way for it? What are the oth…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Hi Michael, I'm using the "contrast" parameter, so I cannot use apeglm with that, as far as I know. The "coef" will not allow me to do eve…
Votes
Comment: Transcript-level differential expression using DESeq2
Comment: Transcript-level differential expression using DESeq2
Answer: how to make a group to apply the data to CAMERA
Answer: how to make a group to apply the data to CAMERA
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
Awards • All
Scholar to Gordon Smyth 45k
Popular Question to andrebolerbarros ▴ 10
Scholar to James W. MacDonald 59k
Scholar to Guido Hooiveld ★ 3.2k
Scholar to Kevin Blighe 3.5k
Locations • All
United States, 12 minutes ago
WEHI, Melbourne, Australia, 16 minutes ago
V&A Waterfront, Cape Town, South Africa, 1 hour ago
United States, 1 hour ago
United Kingdom, 1 hour ago
Traffic: 724 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6