Showing : sva • reset
0
votes
0
replies
67
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
18 days ago • updated 17 days ago georgia.katsoula ▴ 10
0
votes
4
replies
220
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
28 days ago • updated 26 days ago NewBioInfo • 0
1
vote
2
replies
153
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
9 weeks ago Ahdee ▴ 50
0
votes
1
reply
2.1k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 4 months ago by • 0 • written 4.5 years ago by ▴ 10
0
votes
1
reply
250
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 4 months ago by ▴ 50 • written 5 months ago by • 0
0
votes
2
replies
397
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
6 months ago Xiaojie Cheng • 0
0
votes
3
replies
285
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 7 months ago by 3.4k • written 7 months ago by • 0
0
votes
1
reply
215
views
How to set mod0 in sva analysis
sva
updated 8 months ago by ★ 2.7k • written 8 months ago by • 0
2
votes
2
replies
249
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 8 months ago by ▴ 860 • written 8 months ago by • 0
0
votes
0
replies
293
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
9 months ago epibio ▴ 10
1
vote
8
replies
406
views
Error in running Combat function
sva ComBat
updated 8 months ago by 3.4k • written 9 months ago by ▴ 10
0
votes
5
replies
264
views
Variable of interest in combat correction
sva combat
updated 11 months ago by 58k • written 11 months ago by ▴ 10
0
votes
3
replies
267
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 12 months ago by 3.4k • written 12 months ago by • 0
0
votes
10
replies
300
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 13 months ago by 58k • written 13 months ago by • 0
7
votes
6
replies
326
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 17 months ago by ▴ 840 • written 17 months ago by ▴ 10
0
votes
1
reply
163
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 18 months ago by 58k • written 18 months ago by ▴ 20
0
votes
1
reply
171
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 19 months ago by 58k • written 19 months ago by • 0
1
vote
1
reply
198
views
SVA paired samples
SVA EPIC methylation limma
updated 19 months ago by 58k • written 19 months ago by • 0
2
votes
4
replies
266
views
DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 20 months ago by 34k • written 20 months ago by • 0
1
vote
2
replies
238
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 21 months ago by 43k • written 21 months ago by • 0
0
votes
0
replies
535
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
21 months ago anne.bozack • 0
0
votes
1
reply
264
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 22 months ago by ▴ 840 • written 22 months ago by ▴ 10
0
votes
0
replies
220
views
limma-voom group design and its effect on sva
limma voom group-design sva
22 months ago kentfung • 0
0
votes
8
replies
340
views
Error in sva() function: missing values, NaNs produced
sva batch-correction
updated 23 months ago by 58k • written 23 months ago by ▴ 10
0
votes
3
replies
308
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 23 months ago by 25k • written 23 months ago by • 0
2
votes
5
replies
440
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 2.0 years ago by ★ 2.7k • written 2.1 years ago by • 0
0
votes
1
reply
326
views
Handling adjustment variables and surrogate variables in model
sva deseq2
updated 2.1 years ago by 58k • written 2.1 years ago by • 0
1
vote
1
reply
310
views
Bioconductor SVA: two variables of interest
sva
updated 2.1 years ago by 58k • written 2.1 years ago by • 0
4
votes
5
replies
338
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 2.1 years ago by • 0 • written 2.1 years ago by • 0
0
votes
2
replies
268
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 2.1 years ago by 34k • written 2.1 years ago by • 0
0
votes
3
replies
280
views
Design matrix for cohort with samples outside "block"
limma voom sva
2.2 years ago kentfung • 0
0
votes
0
replies
200
views
fsva function does not work without newdat argument
sva
2.2 years ago jakob.wirbel • 0
0
votes
0
replies
285
views
The correct specification of the model matrix to ComBat
ComBat sva
2.2 years ago Sam ▴ 10
7
votes
4
replies
1.7k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 2.2 years ago by 43k • written 2.2 years ago by ▴ 620
0
votes
0
replies
348
views
Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
2.3 years ago kentfung • 0
0
votes
1
reply
394
views
Using surrogate variables as covariates in WGBS differential methylation calling
dmrseq sva DSS
updated 2.3 years ago by ▴ 60 • written 2.4 years ago by • 0
1
vote
8
replies
879
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 2.4 years ago by 34k • written 2.4 years ago by • 0
2
votes
1
reply
516
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
2.4 years ago epibio ▴ 10
5
votes
3
replies
675
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna coexpression sva
updated 2.4 years ago by ★ 2.6k • written 2.4 years ago by ▴ 230
0
votes
1
reply
302
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 2.5 years ago by 34k • written 2.5 years ago by ▴ 20
3
votes
12
replies
1.2k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 2.5 years ago by 58k • written 2.5 years ago by ▴ 10
1
vote
1
reply
345
views
svaseq - over adjustment
svaseq sva
2.6 years ago flippy23 • 0
0
votes
8
replies
504
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 2.6 years ago by 34k • written 2.6 years ago by • 0
1
vote
2
replies
562
views
Normalized transcript/exon counts for network analysis
drimseq dexseq wgcna sva
updated 2.7 years ago by ▴ 90 • written 2.7 years ago by ▴ 20
4
votes
4
replies
721
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 570
0
votes
0
replies
541
views
OpenBLAS issue with ComBat() function of the R SVA package on Torque cluster
sva R OpenBLAS
updated 2.7 years ago by 58k • written 2.7 years ago by • 0
4
votes
2
replies
4.4k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 2.7 years ago by • 0 • written 4.0 years ago by ▴ 60
1
vote
1
reply
392
views
sva correction for MEDIPS
MEDIPS svaseq sva
updated 2.7 years ago by ▴ 570 • written 2.7 years ago by • 0
0
votes
7
replies
597
views
paired sample - SVA model matrix
limma sva paired sample
updated 2.8 years ago by 58k • written 2.8 years ago by • 0
1
vote
1
reply
559
views
Define batch effect variables before removing them or getting rid of hidden surrogate variables
batch effect correction sva proteomics
2.9 years ago Sebastian Hesse ▴ 50
50 results • Page 1 of 1
Recent ...
Replies
Answer: trackViewer peak visualization by Ou, Jianhong ★ 1.2k
Hi, Thanks for using trackViewer to plot your data. In current version of trackViewer, we don't have tracks for peak. There are two chea…
Answer: trackViewer bigWig smoothing by Ou, Jianhong ★ 1.2k
Hi, trackViewer will not recalculate the signals by bins. You may want to try preprocess the signals by other packages such as GenomicRa…
Answer: BLAST-like alignment of a DNAString to a BSgenome? by Hervé Pagès 15k
Hi Charles, One alternative I'm aware of is `annotate::blastSequences()` but I've no experience with it. Best, H.
Answer: trackViewer font by Ou, Jianhong ★ 1.2k
Hi, Try ``` ## set cex to avoid automatic adjust setTrackStyleParam(trackList[[1]], "ylabgp", list(cex=.6)) ``` Let me know if …
Comment: My "Ask a Question" post has been flagged as spam - it is not by ladypurrsia • 0
Thank you very much.
Votes
A: standard error value (lfcSE) returned by DeSeq2
Comment: Model matrix not full rank, then
package ‘destiny’ is not available for Bioconductor version '3.13'
Answer: My "Ask a Question" post has been flagged as spam - it is not
A: DESeq2 for big data sets
Awards • All
Prophet to Lucy ▴ 30
Popular Question to ladypurrsia • 0
Scholar to Mike Smith ★ 5.2k
Popular Question to Sam ▴ 10
Scholar to cannin ▴ 20
Locations • All
Australia, 1 minute ago
Germany, 8 minutes ago
France, 29 minutes ago
Belgium, 35 minutes ago
Peru, 38 minutes ago
Traffic: 288 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