Showing : sva • reset
0
votes
4
replies
170
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 1 hour ago by ▴ 850 • written 6 days ago by • 0
3
votes
6
replies
201
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
7 days ago nhaus ▴ 30
0
votes
2
replies
140
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
16 days ago • updated 15 days ago michelafrancesconi8 • 0
0
votes
4
replies
381
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
17 days ago • updated 16 days ago Lucy ▴ 60
0
votes
8
replies
363
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
6 weeks ago michelafrancesconi8 • 0
0
votes
3
replies
275
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 6 weeks ago by 65k • written 6 weeks ago by ▴ 10
0
votes
5
replies
491
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
0
votes
1
reply
367
views
DESeq2 interaction term + sva
sva DESeq2
updated 3 months ago by 41k • written 4 months ago by ▴ 20
0
votes
2
replies
323
views
combat output NaN
sva
5 months ago maxixian1990 • 0
0
votes
4
replies
550
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 1 day ago by 41k • written 5 months ago by • 0
5
votes
2
replies
691
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
6 months ago Federico ▴ 10
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 17 hours ago by 50k • written 6 months ago by ▴ 10
0
votes
1
reply
428
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 7 months ago by 65k • written 7 months ago by • 0
2
votes
3
replies
1.0k
views
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 8 months ago by 65k • written 8 months ago by ▴ 10
0
votes
2
replies
594
views
Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 9 months ago by • 0
3
votes
3
replies
884
views
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
9 months ago amnahsiddiqa ▴ 10
2
votes
3
replies
1.1k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
0
votes
0
replies
374
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
9 months ago amnahsiddiqa ▴ 10
1
vote
4
replies
1.9k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 6 months ago by • 0 • written 3.1 years ago by • 0
19 results • Page 1 of 1
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Comment: significant difference of p-values with dream() after updating VariancePartition by gabriel.hoffman ▴ 100
See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…
Comment: A ComBat-seq issue: the covariates are confounded by W. Evan Johnson ▴ 850
This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…
Answer: Different number of exons in reference genome affects DEXSeq analysis by Alejandro Reyes ★ 1.9k
Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…
Answer: Adding columns to DEXSeqResults object by Alejandro Reyes ★ 1.9k
I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbo…
Answer: rlog transformation by Michael Love 41k
It is dependent on the other samples in the dataset.
Votes
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
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