Showing : combat • reset
3
votes
8
replies
3.2k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 9.1 years ago by ▴ 30 • written 9.2 years ago by • 0
14
votes
2
replies
3.8k
views
voom with combat
limma voom combat batch effect
updated 9.3 years ago by 53k • written 9.3 years ago by ▴ 10
0
votes
1
reply
1.6k
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray batcheffectcorrection affymetrix microarrays ComBat sva
updated 9.3 years ago by ▴ 420 • written 9.3 years ago by ▴ 840
52
votes
20
replies
51k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 9.4 years ago by • 0 • written 9.9 years ago by ▴ 110
2
votes
3
replies
1.9k
views
comBat/SVA with no "variable of interest" and two batches
combat sva covariates
updated 9.5 years ago by ▴ 420 • written 9.5 years ago by • 0
0
votes
0
replies
1.4k
views
SVA: Using ComBat for synthetic genetic array data
combat sva sga combat batch effect
9.5 years ago John Townsend ▴ 20
7
votes
3
replies
3.8k
views
SVA: Including variable of interest in ComBat model matrix
combat sva SVA sva ComBat batch effect
updated 9.5 years ago by ▴ 870 • written 9.5 years ago by ▴ 20
10
votes
10
replies
5.2k
views
Method for batch correction
combat sva limma
updated 9.5 years ago by ▴ 120 • written 9.6 years ago by ▴ 60
0
votes
1
reply
1.3k
views
Error ,when I use "pa.calls" function on my dataset
panp Combat
9.6 years ago Shamim Sarhadi ▴ 20
1
vote
2
replies
2.4k
views
Evaluation of diagnostic plot resulted from ComBat function regarding batch effect correction of a merged microarray dataset
ComBat diagnostic plot batch effect affymetrix microarrays sva
updated 9.7 years ago by ▴ 870 • written 9.7 years ago by ▴ 840
0
votes
0
replies
2.2k
views
Appropriate implementation of ComBat function for known batch effect correction and alternative methodologies of merging microarray datasets
sva ComBat customcdf affymetrix microarrays limma
9.7 years ago svlachavas ▴ 840
0
votes
2
replies
4.0k
views
Using sva ComBat on DESeq2 Data
deseq2 DE rnaseq sva combat
updated 9.8 years ago by 43k • written 9.8 years ago by • 0
0
votes
6
replies
7.8k
views
ComBat with multiple batches
sva combat 450k
9.8 years ago ben.run974 • 0
4
votes
21
replies
14k
views
DESeq2 and ComBat
deseq2 combat
updated 9.8 years ago by ▴ 610 • written 9.8 years ago by ▴ 100
3
votes
4
replies
6.0k
views
Running Combat in SVA with NA values in matrix
sva combat
9.9 years ago CC ▴ 10
1
vote
1
reply
6.2k
views
Combat generating negative values, should I log2 transform first?
combat batch effect
updated 10.1 years ago by ▴ 870 • written 10.1 years ago by ▴ 60
20
votes
18
replies
6.3k
views
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
limma batch effect ComBat differential gene expression
updated 10.1 years ago by ▴ 870 • written 10.1 years ago by ▴ 840
7
votes
7
replies
11k
views
batch effect : comBat or blocking in limma ?
batch effect combat limma block
updated 10.1 years ago by ★ 7.9k • written 10.1 years ago by ▴ 70
1
vote
1
reply
3.0k
views
sva and svaseq for unsupervised analysis of expression data
sva combat gene expression batch effect rnaseq
updated 10.1 years ago by ▴ 650 • written 10.2 years ago by ▴ 10
0
votes
4
replies
1.9k
views
Reproducibility of results with ComBat
sva combat
updated 10.2 years ago by ▴ 650 • written 10.2 years ago by • 0
1
vote
4
replies
4.2k
views
SVA package - for removing batch effect after DESeq - error in ComBat
sva combat
10.3 years ago GFM ▴ 20
2
votes
7
replies
2.8k
views
ComBat Error: in solve.default(t(des) %*% des) : System is computationally singuar: ...
ComBat sva
10.4 years ago edammer • 0
0
votes
6
replies
2.2k
views
Problem in analysing microarray data with ComBat
combat
updated 2.6 years ago by ▴ 870 • written 10.4 years ago by • 0
0
votes
2
replies
6.2k
views
Combat in R (SVA package) error message
combat software error
updated 10.5 years ago by ★ 3.0k • written 10.5 years ago by • 0
0
votes
4
replies
7.5k
views
ComBat: Error non-conformable arguments
ComBat
updated 10.5 years ago by 68k • written 10.5 years ago by • 0
2
votes
6
replies
4.8k
views
Combat for batch effects
combat
10.6 years ago zhouxiuqing • 0
1
vote
2
replies
1.9k
views
Question about the proper way to combine Illumina Human HT-12 v4 expression datasets from different labs
combat batch effect
10.6 years ago jaro.slamecka ▴ 140
1
vote
1
reply
1.9k
views
ComBat (SVA) Application - Two Technical Effects
sva ComBat
updated 10.8 years ago by ▴ 610 • written 10.8 years ago by ▴ 370
0
votes
0
replies
925
views
comBat for multiple diseases
comBat
10.8 years ago sathyabaarathi • 0
0
votes
2
replies
3.1k
views
Remove batch effect - condition partially confounded by data
combat differential gene expression sva
updated 10.8 years ago by ▴ 650 • written 10.8 years ago by • 0
0
votes
0
replies
1.3k
views
How can I use Combat correction parameters from one data set to adjust a new data set with the same batches
combat sva papramters
10.9 years ago p.yishai • 0
4
votes
4
replies
5.2k
views
sva::ComBat without covariate of interest?
sva combat
updated 10.9 years ago by ▴ 870 • written 11.0 years ago by ▴ 110
2
votes
2
replies
4.1k
views
ComBat: should the variable of interest be included into model matrix
ComBat
updated 10.9 years ago by ▴ 870 • written 10.9 years ago by ▴ 10
5
votes
2
replies
3.7k
views
ComBat - Including variable of interest in model matrix?
combat sva
updated 11.0 years ago by ▴ 650 • written 11.0 years ago by ▴ 10
1
vote
3
replies
7.4k
views
Combat - error - system is computationally singular
combat software error rnaseq complex-design
updated 11.0 years ago by ★ 3.0k • written 11.0 years ago by ▴ 40
85 results • Page 2 of 2
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Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Comment: deseq2 filter the low counts by empty_mt • 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions by Michael Love 43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
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