Showing : SVA • reset
1
vote
2
replies
126
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
4 weeks ago Ahdee ▴ 50
0
votes
1
reply
2.0k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 3 months ago by • 0 • written 4.4 years ago by ▴ 10
0
votes
1
reply
211
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 3 months ago by ▴ 50 • written 3 months ago by • 0
0
votes
2
replies
326
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
5 months ago Xiaojie Cheng • 0
0
votes
3
replies
263
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 6 months ago by 3.4k • written 6 months ago by • 0
0
votes
1
reply
186
views
How to set mod0 in sva analysis
sva
updated 7 months ago by ★ 2.7k • written 7 months ago by • 0
2
votes
2
replies
226
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 7 months ago by ▴ 830 • written 7 months ago by • 0
0
votes
0
replies
273
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
8 months ago epibio ▴ 10
1
vote
8
replies
375
views
Error in running Combat function
sva ComBat
updated 7 months ago by 3.4k • written 8 months ago by ▴ 10
0
votes
5
replies
225
views
Variable of interest in combat correction
sva combat
updated 10 months ago by 58k • written 10 months ago by ▴ 10
0
votes
3
replies
251
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 11 months ago by 3.4k • written 11 months ago by • 0
0
votes
10
replies
282
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 12 months ago by 58k • written 12 months ago by • 0
7
votes
6
replies
309
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 16 months ago by ▴ 840 • written 16 months ago by ▴ 10
0
votes
1
reply
151
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 17 months ago by 58k • written 17 months ago by ▴ 20
0
votes
1
reply
160
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 18 months ago by 58k • written 18 months ago by • 0
1
vote
1
reply
180
views
SVA paired samples
SVA EPIC methylation limma
updated 18 months ago by 58k • written 18 months ago by • 0
2
votes
4
replies
247
views
DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 19 months ago by 34k • written 19 months ago by • 0
1
vote
2
replies
216
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 20 months ago by 43k • written 20 months ago by • 0
0
votes
0
replies
503
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
20 months ago anne.bozack • 0
0
votes
1
reply
250
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 21 months ago by ▴ 840 • written 21 months ago by ▴ 10
0
votes
0
replies
208
views
limma-voom group design and its effect on sva
limma voom group-design sva
21 months ago kentfung • 0
0
votes
8
replies
321
views
Error in sva() function: missing values, NaNs produced
sva batch-correction
updated 22 months ago by 58k • written 22 months ago by ▴ 10
0
votes
3
replies
291
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 22 months ago by 25k • written 22 months ago by • 0
2
votes
5
replies
422
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 23 months ago by ★ 2.7k • written 24 months ago by • 0
0
votes
1
reply
308
views
Handling adjustment variables and surrogate variables in model
sva deseq2
updated 2.0 years ago by 58k • written 2.0 years ago by • 0
1
vote
1
reply
293
views
Bioconductor SVA: two variables of interest
sva
updated 2.0 years ago by 58k • written 2.0 years ago by • 0
4
votes
5
replies
322
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 2.0 years ago by • 0 • written 2.0 years ago by • 0
0
votes
2
replies
255
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
263
views
Design matrix for cohort with samples outside "block"
limma voom sva
2.1 years ago kentfung • 0
0
votes
0
replies
192
views
fsva function does not work without newdat argument
sva
2.1 years ago jakob.wirbel • 0
0
votes
0
replies
276
views
The correct specification of the model matrix to ComBat
ComBat sva
2.1 years ago Sam ▴ 10
7
votes
4
replies
1.6k
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
324
views
Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
2.2 years ago kentfung • 0
0
votes
1
reply
374
views
Using surrogate variables as covariates in WGBS differential methylation calling
dmrseq sva DSS
updated 2.3 years ago by ▴ 60 • written 2.3 years ago by • 0
1
vote
8
replies
847
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 2.3 years ago by 34k • written 2.3 years ago by • 0
2
votes
1
reply
483
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
2.3 years ago epibio ▴ 10
5
votes
3
replies
651
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna coexpression sva
updated 2.3 years ago by ★ 2.6k • written 2.3 years ago by ▴ 230
0
votes
1
reply
288
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 2.4 years ago by 34k • written 2.4 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 2.4 years ago by 58k • written 2.4 years ago by ▴ 10
1
vote
1
reply
329
views
svaseq - over adjustment
svaseq sva
2.5 years ago flippy23 • 0
0
votes
8
replies
487
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 2.5 years ago by 34k • written 2.5 years ago by • 0
1
vote
2
replies
541
views
Normalized transcript/exon counts for network analysis
drimseq dexseq wgcna sva
updated 2.6 years ago by ▴ 90 • written 2.6 years ago by ▴ 20
4
votes
4
replies
701
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 2.6 years ago by 43k • written 2.6 years ago by ▴ 570
0
votes
0
replies
521
views
OpenBLAS issue with ComBat() function of the R SVA package on Torque cluster
sva R OpenBLAS
updated 2.6 years ago by 58k • written 2.6 years ago by • 0
4
votes
2
replies
4.2k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 2.6 years ago by • 0 • written 3.9 years ago by ▴ 60
1
vote
1
reply
379
views
sva correction for MEDIPS
MEDIPS svaseq sva
updated 2.6 years ago by ▴ 550 • written 2.6 years ago by • 0
0
votes
7
replies
580
views
paired sample - SVA model matrix
limma sva paired sample
updated 2.7 years ago by 58k • written 2.7 years ago by • 0
1
vote
1
reply
546
views
Define batch effect variables before removing them or getting rid of hidden surrogate variables
batch effect correction sva proteomics
2.8 years ago Sebastian Hesse ▴ 50
1
vote
10
replies
2.4k
views
SVAseq and DESeq2 workflow
sva deseq2
updated 2.9 years ago by 34k • written 2.9 years ago by • 0
0
votes
0
replies
310
views
Sva for tumor cellular heterogeneity
limma sva
2.9 years ago chp950 • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Error in makeTxDbFromGFF(txomeInfo$gtf) by Michael Love 34k
I see that tximeta found a linked transcriptome. Can you show this part of your code as well? How did you create the `linkedTxome`?
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Gordon Smyth 43k
You need to start by doing an ordinary paired analysis.
Comment: Recalculated abundance data output table with DEseq2 by Michael Love 34k
Yes, DESeq() then results(). When you print the table it will say MLE. No we don’t have a function to do that.
Comment: Recalculated abundance data output table with DEseq2 by michael.morash • 0
Thanks for getting back to me so quickly. The final comparison we are looking to report are the effects of filtering out low count genes us…
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Field -Ye • 0
Hi Professor Smyth, Thank you for pointing me to your previous publication. I went through the verbal part and found you did pursue the DG…
Votes
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2
Comment: How to build a GRangesList where each GRanges element is a CDS coordinate of gen
Awards • All
Scholar to Rory Stark ★ 4.1k
Scholar to jbnrodriguez • 0
Scholar to Yang Liao ▴ 260
Scholar to James W. MacDonald 58k
Teacher to Michael Love 34k
Locations • All
Hong Kong, 1 hour ago
San Diego, 1 hour ago
China, 1 hour ago
United States, 1 hour ago
Australia, 2 hours ago
Traffic: 237 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