Showing : sva • reset
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112
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SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 4 weeks ago by 63k • written 4 weeks ago by • 0
1
vote
3
replies
237
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bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 6 weeks ago by 63k • written 6 weeks ago by • 0
0
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2
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267
views
Fluidigm Data Batch Correction
sva limma
updated 9 weeks ago by 48k • written 10 weeks ago by • 0
2
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3
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366
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how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq RNASeqData sva limma
12 weeks ago amnahsiddiqa • 0
1
vote
3
replies
437
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 12 weeks ago by ★ 3.4k • written 12 weeks ago by • 0
0
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0
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157
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
12 weeks ago amnahsiddiqa • 0
0
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1
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239
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 6 months ago by ★ 3.4k • written 6 months ago by • 0
2
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2
replies
393
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
7 months ago Hatchet • 0
5
votes
2
replies
461
views
Sva and batch effect
limma BatchEffect sva
updated 7 months ago by 48k • written 7 months ago by • 0
0
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2
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504
views
DESeq2 LFC changes sign after adjusting for surrogates
sva DESeq2
13 months ago Marie • 0
2
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9
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1.1k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 14 months ago by 63k • written 14 months ago by • 0
1
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0
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498
views
Why does surrogate variable confound with variable given in mod?
sva
14 months ago shdam ▴ 10
1
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3
replies
970
views
Error in shrinkage for DESeq2
sva DESeq2
15 months ago Kent • 0
4
votes
3
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8.1k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 16 months ago by • 0 • written 6.0 years ago by ▴ 60
1
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1
reply
525
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq sva DESeq2
updated 16 months ago by 63k • written 16 months ago by • 0
1
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2
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1.1k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
16 months ago takemoto • 0
0
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1
reply
592
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 17 months ago by 48k • written 17 months ago by • 0
1
vote
1
reply
767
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 19 months ago by ★ 3.4k • written 19 months ago by • 0
1
vote
4
replies
1.2k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2 sva
19 months ago Clay • 0
0
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0
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811
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 20 months ago by 63k • written 20 months ago by • 0
0
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5
replies
2.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 20 months ago by ★ 3.4k • written 2.5 years ago by • 0
0
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0
replies
588
views
SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
24 months ago georgia.katsoula ▴ 40
1
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4
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4.4k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
2.0 years ago NewBioInfo ▴ 10
1
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2
replies
999
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
2.1 years ago Ahdee ▴ 50
0
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1
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3.1k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA combat sva leek
updated 2.3 years ago by • 0 • written 6.4 years ago by ▴ 10
0
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1
reply
1.3k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA impute sva
updated 2.3 years ago by ▴ 50 • written 2.3 years ago by • 0
1
vote
3
replies
1.2k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 2.5 years ago by 3.8k • written 2.5 years ago by • 0
0
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1
reply
943
views
How to set mod0 in sva analysis
sva
updated 2.6 years ago by ★ 3.0k • written 2.6 years ago by • 0
2
votes
2
replies
775
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 2.6 years ago by ★ 3.4k • written 2.6 years ago by • 0
0
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0
replies
746
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
2.7 years ago epibio ▴ 10
1
vote
8
replies
1.1k
views
Error in running Combat function
sva ComBat
updated 2.7 years ago by 3.8k • written 2.7 years ago by ▴ 10
0
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5
replies
775
views
Variable of interest in combat correction
sva combat
updated 2.9 years ago by 63k • written 2.9 years ago by ▴ 10
0
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3
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776
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 3.0 years ago by 3.8k • written 3.0 years ago by • 0
0
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10
replies
904
views
Running SVA changes format of time variable in model
sva proxitct hms
updated 3.0 years ago by 63k • written 3.0 years ago by • 0
7
votes
6
replies
1.2k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 3.4 years ago by ▴ 840 • written 3.4 years ago by ▴ 10
0
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1
reply
574
views
SVA for visualisation purposes
sva svaseq surrogate variable analysis
updated 3.4 years ago by 63k • written 3.4 years ago by ▴ 20
0
votes
1
reply
741
views
Adjusting for unwanted variation in DESeq2
DESeq2 deseq2 sva rna-seq differential expression anlaysis
updated 3.5 years ago by 63k • written 3.5 years ago by • 0
1
vote
1
reply
703
views
SVA paired samples
SVA EPIC methylation limma
updated 3.6 years ago by 63k • written 3.6 years ago by • 0
2
votes
4
replies
787
views
DESeq2 - problem with inferring correct results.
deseq2 rnaseq sva fdrtool ihw
updated 3.6 years ago by 40k • written 3.6 years ago by • 0
1
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2
replies
696
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 3.7 years ago by 48k • written 3.7 years ago by • 0
0
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0
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1.6k
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
3.7 years ago anne.bozack • 0
0
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1
reply
672
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 3.8 years ago by ▴ 840 • written 3.8 years ago by ▴ 10
0
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0
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644
views
limma-voom group design and its effect on sva
limma voom group-design sva
3.8 years ago kentfung ▴ 10
0
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8
replies
1.1k
views
Error in sva() function: missing values, NaNs produced
sva batch-correction
updated 3.9 years ago by 63k • written 3.9 years ago by ▴ 10
0
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3
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770
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 3.9 years ago by 25k • written 3.9 years ago by • 0
2
votes
5
replies
1.0k
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 4.0 years ago by ★ 3.0k • written 4.0 years ago by • 0
0
votes
1
reply
832
views
Handling adjustment variables and surrogate variables in model
sva deseq2
updated 4.0 years ago by 63k • written 4.0 years ago by • 0
1
vote
1
reply
942
views
Bioconductor SVA: two variables of interest
sva
updated 4.0 years ago by 63k • written 4.0 years ago by • 0
4
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5
replies
734
views
Design matrix with intercept for multiple cluster comparison
limma sva
updated 4.1 years ago by • 0 • written 4.1 years ago by ▴ 10
0
votes
2
replies
904
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 4.1 years ago by 40k • written 4.1 years ago by • 0
50 results • Page 1 of 1
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Comment: DataFrame Construction With Non-standard Column by Hervé Pagès 16k
SimpleList is a List derivative and List derivatives in general don't need protection. For example, a GRangesList object (which is also a L…
Answer: Deseq2, how to model design for comparing Mutant mouse at age 14 days versus Mu by swbarnes2 ★ 1.3k
The Status grouping you show above is good to use if you want to simply compare one subset of samples to another subset. The ~Genotype +…
Answer: Remove duplicates of colData in TreeSummarizedExperiment by Michael Love 40k
Copying my code from Slack for posterity. James' code is more streamlined for this step I think. ``` # make a dataset that has duplicate s…
Comment: DataFrame Construction With Non-standard Column by James W. MacDonald 63k
Oh, ok. I understand. Technically both should work according to what the help page for `DataFrame` says (both `SimpleList` and `list` have …
Comment: DeSeq2 design fails (full model matrix is less than full rank) by Basti ▴ 720
As recommended, you can only perform ~group. You can use contrasts do perform the comparison AA5 vs FHIN1 (see [DESeq2 vignette][1]), but t…
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Answer: Further analysis after limma regression output
A: collapseReplicates in DESeq2
Answer: DataFrame Construction With Non-standard Column
Steps needed to change design (relevel factors) in DESeq2
Steps needed to change design (relevel factors) in DESeq2
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