Showing : combat • reset
0
votes
4
replies
439
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
5 weeks ago Lucy ▴ 60
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 3.2 years ago by • 0
5
votes
2
replies
769
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
7 months ago Federico ▴ 10
0
votes
0
replies
487
views
combat for batch effect correction in EPIC array data
Epigenetics combat EPIC
14 months ago • updated 13 months ago Jitendra ▴ 10
0
votes
6
replies
1.6k
views
Problem in analysing microarray data with ComBat
combat
updated 14 months ago by ▴ 850 • written 9.0 years ago by • 0
5
votes
8
replies
2.4k
views
Combat and dds Object
DESeq2 combat
updated 15 months ago by ★ 4.1k • written 2.8 years ago by ▴ 40
1
vote
2
replies
1.6k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
24 months ago • updated 23 months ago takemoto • 0
0
votes
1
reply
942
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.1 years ago by 50k • written 2.1 years ago by • 0
1
vote
4
replies
5.9k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
2.6 years ago NewBioInfo ▴ 10
0
votes
0
replies
702
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix comBat
3.1 years ago joannew • 0
8
votes
18
replies
12k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 3.2 years ago by • 0 • written 4.6 years ago by ▴ 10
1
vote
8
replies
1.4k
views
Error in running Combat function
sva ComBat
updated 3.3 years ago by ★ 3.9k • written 3.3 years ago by ▴ 10
0
votes
5
replies
1.0k
views
Variable of interest in combat correction
sva combat
updated 3.5 years ago by 65k • written 3.5 years ago by ▴ 10
0
votes
3
replies
1.1k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
7
votes
6
replies
1.7k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 4.0 years ago by ▴ 850 • written 4.0 years ago by ▴ 10
1
vote
2
replies
936
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 4.3 years ago by 50k • written 4.3 years ago by • 0
0
votes
0
replies
2.0k
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
4.4 years ago anne.bozack • 0
0
votes
1
reply
981
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 4.4 years ago by ★ 3.9k • written 4.4 years ago by • 0
0
votes
1
reply
899
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 4.4 years ago by ▴ 850 • written 4.4 years ago by ▴ 10
0
votes
3
replies
997
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 4.5 years ago by 25k • written 4.5 years ago by • 0
2
votes
2
replies
1.3k
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 4.6 years ago by 42k • written 4.6 years ago by ▴ 10
2
votes
3
replies
1.1k
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 4.7 years ago by ★ 1.3k • written 4.7 years ago by ▴ 80
0
votes
2
replies
1.1k
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 4.7 years ago by 42k • written 4.7 years ago by • 0
0
votes
0
replies
815
views
The correct specification of the model matrix to ComBat
ComBat sva
4.7 years ago Sam ▴ 10
0
votes
6
replies
1.8k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 4.7 years ago by ▴ 270 • written 4.8 years ago by ▴ 670
7
votes
4
replies
3.9k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 4.8 years ago by 50k • written 4.8 years ago by ▴ 670
4
votes
16
replies
4.6k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 4.9 years ago by 42k • written 4.9 years ago by ▴ 10
3
votes
12
replies
3.2k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 10
0
votes
0
replies
810
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 5.6 years ago by 50k • written 5.6 years ago by • 0
0
votes
2
replies
1.4k
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 5.6 years ago by 42k • written 5.6 years ago by • 0
0
votes
0
replies
935
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
5.7 years ago jmsendoya • 0
0
votes
1
reply
1.8k
views
A problem in using Combat
sva combat
updated 5.9 years ago by ▴ 850 • written 5.9 years ago by • 0
1
vote
1
reply
2.1k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 6.3 years ago by 50k • written 9.1 years ago by ▴ 140
1
vote
9
replies
2.5k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
6.3 years ago jaro.slamecka ▴ 140
0
votes
8
replies
2.3k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 6.4 years ago by • 0 • written 8.8 years ago by • 0
0
votes
0
replies
1.1k
views
SVA/Combat without fitting an intercept
sva combat batch effect limma
6.5 years ago Eddie Imada • 0
0
votes
1
reply
1.2k
views
Combat prior plots good enough?
combat combat sva
6.6 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
2
votes
5
replies
2.8k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 6.6 years ago by ▴ 850 • written 6.6 years ago by • 0
2
votes
5
replies
5.9k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 20
1
vote
1
reply
1.8k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 6.8 years ago by 65k • written 6.8 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
6.8 years ago DataFanatic ▴ 10
0
votes
4
replies
2.4k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 6.9 years ago by 42k • written 6.9 years ago by • 0
0
votes
0
replies
1.3k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
7.0 years ago svlachavas ▴ 830
1
vote
1
reply
1.1k
views
How to interpret the SVA results
SVA combat RNA-seq
updated 7.1 years ago by 65k • written 7.1 years ago by • 0
10
votes
4
replies
3.0k
views
Adjust for multiple batches using combat
combat sva limma
updated 7.2 years ago by ★ 28k • written 7.2 years ago by • 0
3
votes
4
replies
2.8k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 7.2 years ago by 42k • written 7.2 years ago by ▴ 10
0
votes
0
replies
1.1k
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
7.2 years ago Ryan C. Thompson ★ 7.9k
0
votes
6
replies
1.7k
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
7.5 years ago User34591 • 0
5
votes
2
replies
7.2k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 7.6 years ago by ▴ 70 • written 7.6 years ago by ▴ 30
5
votes
3
replies
3.9k
views
about SVA: matrix of corrected expression values
SVA COMBAT
7.6 years ago Bogdan ▴ 670
50 results • Page 1 of 1
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Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma by Gordon Smyth 50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Comment: Extremely small p-values using Limma for proteomic data by Abbey • 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
Probably. I would not expect such large fold changes. But without seeing your code, who knows?
Comment: Extremely small p-values using Limma for proteomic data by Abbey • 0
Thank you James! This worked to fix the p-values. However, the plot still looks one-sided... any idea what's going on with the left side?…
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Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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