Showing : ComBat • reset
0
votes
4
replies
883
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
8 months ago Lucy ▴ 60
5
votes
2
replies
1.8k
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
15 months ago Federico ▴ 10
0
votes
0
replies
654
views
combat for batch effect correction in EPIC array data
Epigenetics combat EPIC
21 months ago Jitendra ▴ 10
1
vote
2
replies
2.1k
views
Is it necessary to standardize Combat in R?
RNA Combat sva R
2.6 years ago takemoto • 0
0
votes
1
reply
1.3k
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.7 years ago by 52k • written 2.7 years ago by • 0
1
vote
4
replies
7.2k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
3.3 years ago • updated 3.2 years ago NewBioInfo ▴ 10
5
votes
8
replies
3.2k
views
Combat and dds Object
DESeq2 combat
updated 22 months ago by ★ 4.6k • written 3.4 years ago by ▴ 50
0
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0
replies
875
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix comBat
3.7 years ago joannew • 0
1
vote
4
replies
2.7k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 14 months ago by • 0 • written 3.8 years ago by • 0
1
vote
8
replies
1.8k
views
Error in running Combat function
sva ComBat
updated 3.9 years ago by ★ 4.0k • written 3.9 years ago by ▴ 10
0
votes
5
replies
1.3k
views
Variable of interest in combat correction
sva combat
updated 4.1 years ago by 67k • written 4.1 years ago by ▴ 10
0
votes
3
replies
1.3k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by • 0
7
votes
6
replies
2.2k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 4.6 years ago by ▴ 870 • written 4.6 years ago by ▴ 10
1
vote
2
replies
1.2k
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 4.9 years ago by 52k • written 4.9 years ago by • 0
0
votes
0
replies
2.4k
views
adjusting for batch using ComBat (sva) - singularity error
microarray combat sva batch effects
5.0 years ago anne.bozack • 0
0
votes
1
reply
1.2k
views
Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by • 0
0
votes
1
reply
1.1k
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 5.0 years ago by ▴ 870 • written 5.0 years ago by ▴ 10
0
votes
3
replies
1.2k
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 5.1 years ago by 25k • written 5.1 years ago by • 0
8
votes
18
replies
14k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 3.8 years ago by • 0 • written 5.2 years ago by ▴ 10
2
votes
2
replies
1.6k
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 10
2
votes
3
replies
1.3k
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 5.3 years ago by ★ 1.4k • written 5.3 years ago by ▴ 80
0
votes
2
replies
1.4k
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
0
replies
948
views
The correct specification of the model matrix to ComBat
ComBat sva
5.4 years ago Sam ▴ 10
0
votes
6
replies
2.0k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 5.4 years ago by ▴ 270 • written 5.4 years ago by ▴ 670
8
votes
4
replies
4.5k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 5.4 years ago by 52k • written 5.4 years ago by ▴ 670
4
votes
16
replies
5.9k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 10
3
votes
12
replies
4.0k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 5.7 years ago by 67k • written 5.7 years ago by ▴ 10
0
votes
0
replies
967
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 6.2 years ago by 52k • written 6.2 years ago by • 0
0
votes
2
replies
1.6k
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
votes
0
replies
1.1k
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
6.3 years ago jmsendoya • 0
0
votes
1
reply
2.2k
views
A problem in using Combat
sva combat
updated 6.5 years ago by ▴ 870 • written 6.5 years ago by • 0
1
vote
1
reply
2.2k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 6.9 years ago by 52k • written 9.8 years ago by ▴ 140
1
vote
9
replies
3.0k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
6.9 years ago jaro.slamecka ▴ 140
0
votes
8
replies
2.6k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 7.0 years ago by • 0 • written 9.4 years ago by • 0
0
votes
0
replies
1.2k
views
SVA/Combat without fitting an intercept
sva combat batch effect limma
7.2 years ago Eddie Imada • 0
0
votes
1
reply
1.4k
views
Combat prior plots good enough?
combat combat sva
7.2 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
2
votes
5
replies
3.3k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 7.2 years ago by ▴ 870 • written 7.2 years ago by • 0
2
votes
5
replies
6.8k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 20
1
vote
1
reply
2.1k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 7.4 years ago by 67k • written 7.4 years ago by ▴ 10
0
votes
0
replies
1.5k
views
Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
7.4 years ago DataFanatic ▴ 10
0
votes
4
replies
2.7k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
votes
0
replies
1.4k
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0 limma batch effect affymetrix microarrays ComBat
7.6 years ago svlachavas ▴ 840
1
vote
1
reply
1.2k
views
How to interpret the SVA results
SVA combat RNA-seq
updated 7.7 years ago by 67k • written 7.7 years ago by • 0
10
votes
4
replies
3.4k
views
Adjust for multiple batches using combat
combat sva limma
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
3
votes
4
replies
3.2k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 10
0
votes
0
replies
1.3k
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat rnaseq sva
7.9 years ago Ryan C. Thompson ★ 7.9k
0
votes
6
replies
2.0k
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
8.2 years ago User34591 • 0
5
votes
2
replies
7.6k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 8.2 years ago by ▴ 70 • written 8.2 years ago by ▴ 30
5
votes
3
replies
4.2k
views
about SVA: matrix of corrected expression values
SVA COMBAT
8.2 years ago Bogdan ▴ 670
3
votes
8
replies
2.7k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 8.3 years ago by ▴ 30 • written 8.3 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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