Showing : sva • reset
0
votes
2
replies
169
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
7 weeks ago • updated 6 weeks ago Xiaojie Cheng • 0
0
votes
3
replies
143
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 8 weeks ago by 2.9k • written 8 weeks ago by • 0
0
votes
1
reply
76
views
How to set mod0 in sva analysis
sva
updated 12 weeks ago by ★ 2.7k • written 12 weeks ago by • 0
2
votes
2
replies
122
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 12 weeks ago by ▴ 630 • written 12 weeks ago by • 0
0
votes
0
replies
184
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3 months ago Papyrus ▴ 10
1
vote
8
replies
279
views
Error in running Combat function
sva ComBat
updated 3 months ago by 2.9k • written 3 months ago by ▴ 10
0
votes
5
replies
132
views
Variable of interest in combat correction
sva combat
updated 6 months ago by 56k • written 6 months ago by ▴ 10
0
votes
3
replies
171
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 7 months ago by 2.9k • written 7 months ago by • 0
0
votes
10
replies
173
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 8 months ago by 56k • written 8 months ago by • 0
7
votes
6
replies
204
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 12 months ago by ▴ 840 • written 12 months ago by ▴ 10
0
votes
1
reply
92
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 13 months ago by 56k • written 13 months ago by ▴ 20
0
votes
1
reply
108
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 14 months ago by 56k • written 14 months ago by • 0
1
vote
1
reply
105
views
SVA paired samples
SVA EPIC methylation limma
updated 14 months ago by 56k • written 14 months ago by • 0
2
votes
4
replies
147
views
DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 14 months ago by 32k • written 14 months ago by • 0
1
vote
2
replies
142
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 15 months ago by 42k • written 15 months ago by • 0
0
votes
0
replies
351
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
16 months ago anne.bozack • 0
0
votes
1
reply
169
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 17 months ago by ▴ 840 • written 17 months ago by ▴ 10
0
votes
0
replies
149
views
limma-voom group design and its effect on sva
limma voom group-design sva
17 months ago kentfung • 0
0
votes
8
replies
210
views
Error in sva() function: missing values, NaNs produced
sva batch-correction
updated 18 months ago by 56k • written 18 months ago by ▴ 10
0
votes
3
replies
204
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 18 months ago by 25k • written 18 months ago by • 0
2
votes
5
replies
325
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 19 months ago by ★ 2.7k • written 19 months ago by • 0
0
votes
1
reply
217
views
Handling adjustment variables and surrogate variables in model
sva deseq2
updated 20 months ago by 56k • written 20 months ago by • 0
1
vote
1
reply
224
views
Bioconductor SVA: two variables of interest
sva
updated 20 months ago by 56k • written 20 months ago by • 0
4
votes
5
replies
261
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 20 months ago by • 0 • written 20 months ago by • 0
0
votes
2
replies
186
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 20 months ago by 32k • written 20 months ago by • 0
0
votes
3
replies
203
views
Design matrix for cohort with samples outside "block"
limma voom sva
21 months ago kentfung • 0
0
votes
0
replies
135
views
fsva function does not work without newdat argument
sva
21 months ago jakob.wirbel • 0
0
votes
0
replies
218
views
The correct specification of the model matrix to ComBat
ComBat sva
21 months ago Sam ▴ 10
7
votes
4
replies
1.3k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 22 months ago by 42k • written 22 months ago by ▴ 610
0
votes
0
replies
251
views
Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
22 months ago kentfung • 0
0
votes
1
reply
272
views
Using surrogate variables as covariates in WGBS differential methylation calling
dmrseq sva DSS
updated 23 months ago by ▴ 60 • written 23 months ago by • 0
1
vote
8
replies
652
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 23 months ago by 32k • written 23 months ago by • 0
2
votes
1
reply
379
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
23 months ago Papyrus ▴ 10
5
votes
3
replies
499
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna coexpression sva
updated 23 months ago by ★ 2.6k • written 23 months ago by ▴ 230
0
votes
1
reply
228
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 2.0 years ago by 32k • written 2.0 years ago by ▴ 20
3
votes
12
replies
919
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 2.0 years ago by 56k • written 2.0 years ago by ▴ 10
1
vote
1
reply
246
views
svaseq - over adjustment
svaseq sva
2.1 years ago flippy23 • 0
0
votes
8
replies
356
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 2.1 years ago by 32k • written 2.1 years ago by • 0
1
vote
2
replies
422
views
Normalized transcript/exon counts for network analysis
drimseq dexseq wgcna sva
updated 2.2 years ago by ▴ 80 • written 2.2 years ago by ▴ 10
4
votes
4
replies
589
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 2.2 years ago by 42k • written 2.2 years ago by ▴ 570
0
votes
0
replies
422
views
OpenBLAS issue with ComBat() function of the R SVA package on Torque cluster
sva R OpenBLAS
updated 2.2 years ago by 56k • written 2.2 years ago by • 0
4
votes
2
replies
3.8k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 2.3 years ago by • 0 • written 3.6 years ago by ▴ 60
1
vote
1
reply
293
views
sva correction for MEDIPS
MEDIPS svaseq sva
updated 2.3 years ago by ▴ 550 • written 2.3 years ago by • 0
0
votes
7
replies
496
views
paired sample - SVA model matrix
limma sva paired sample
updated 2.4 years ago by 56k • written 2.4 years ago by • 0
1
vote
1
reply
471
views
Define batch effect variables before removing them or getting rid of hidden surrogate variables
batch effect correction sva proteomics
2.5 years ago Sebastian Hesse ▴ 50
1
vote
10
replies
1.8k
views
SVAseq and DESeq2 workflow
sva deseq2
updated 2.6 years ago by 32k • written 2.6 years ago by • 0
0
votes
0
replies
262
views
Sva for tumor cellular heterogeneity
limma sva
2.6 years ago chp950 • 0
0
votes
2
replies
569
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 2.6 years ago by 32k • written 2.6 years ago by • 0
0
votes
0
replies
313
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
2.7 years ago jmsendoya • 0
0
votes
1
reply
565
views
A problem in using Combat
sva combat
updated 2.9 years ago by ▴ 840 • written 2.9 years ago by • 0
50 results • Page 1 of 1
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Answer: Effect of feature number on adjusted p-values by Aaron Lun ★ 26k
> I assume this will have an impact on identifying significant gene regulation events, as p-value correction for multiple testing (both BH …
Answer: After having the output from SingleR for cell type annotation, what's the next s by Aaron Lun ★ 26k
**SingleR** is a well-behaved classification method in that each cell's assigned cell type is independent of the presence/behavior of other…
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I agree with ATpoint. I also think your assumption is incorrect. Clusters with more expressed genes will generally have more DE genes at a …
Comment: Effect of feature number on adjusted p-values by ATpoint ▴ 630
Wouldn't a proper DE analysis have a single count matrix with all involved genes and samples (or cell type, clusters, or whatever you analy…
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Thanks so much for posting this! Have been going crazy all afternoon trying to install a package!
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Comment: How to download the ChAMP dependency ChAMPdata
Bioconductor Award for Outstanding Documentation
C: With DESeq2 "Not full rank" Error with design ~ line + time + condition
C: With DESeq2 "Not full rank" Error with design ~ line + time + condition
What does dba.PCA in DiffBind exactly do?
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