Showing : removebatcheffect • reset
4
votes
7
replies
3.2k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
6 months ago • updated 22 days ago massimo ▴ 10
2
votes
2
replies
722
views
Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
13 months ago sukeshinik5 ▴ 20
17
votes
9
replies
8.2k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 13 months ago by 68k • written 9.4 years ago by ▴ 10
4
votes
4
replies
1.7k
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma adjustment voom removeBatchEffect covariates
16 months ago sukeshinik5 ▴ 20
0
votes
2
replies
1.7k
views
Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
2.8 years ago dqt • 0
0
votes
5
replies
5.9k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.8 years ago by ★ 5.0k • written 4.6 years ago by • 0
0
votes
1
reply
1.2k
views
Should the design matrix for removeBatchEffect include an intercept?
removeBatchEffect limma
updated 5.7 years ago by 53k • written 5.7 years ago by ▴ 10
5
votes
7
replies
3.6k
views
logCPM to CPM conversion after removeBatchEffect()
edger removeBatchEffect cpm logCPM limma
6.4 years ago altintas.ali • 0
1
vote
6
replies
2.3k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 120
2
votes
5
replies
5.4k
views
Batch Effect Correction
batch effect removebatcheffect edgeR rld DEseq2
7.3 years ago Antonio Ahn ▴ 10
1
vote
1
reply
2.0k
views
Batch effect removal before SC3?
SC3 batch effect removebatcheffect
updated 7.9 years ago by ▴ 150 • written 7.9 years ago by ▴ 10
11
votes
8
replies
13k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 8.1 years ago by 53k • written 8.1 years ago by ▴ 80
9
votes
8
replies
11k
views
removeBatchEffect options: design and covariates
limma removebatcheffect
updated 8.1 years ago by 53k • written 11.2 years ago by ▴ 550
0
votes
1
reply
2.9k
views
Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactly singular: U[4,4] = 0
sva R removebatcheffect
8.4 years ago aina.jene ▴ 10
2
votes
2
replies
2.6k
views
SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
sva removebatcheffect R
updated 8.5 years ago by ▴ 130 • written 8.5 years ago by ▴ 10
1
vote
3
replies
1.8k
views
Re-use limma beta coefficients
limma removebatcheffect
8.9 years ago Keifa ▴ 10
3
votes
6
replies
3.4k
views
is it necessary to check batch effect in this case? and how to?
svaseq combat sva RANseq batcheffect removebatcheffect
updated 9.0 years ago by ▴ 50 • written 9.0 years ago by ▴ 10
0
votes
3
replies
1.9k
views
How to remove nested batch effects with removeBatchEffect?
edgeR removeBatchEffect nested design
updated 9.0 years ago by ★ 29k • written 9.0 years ago by ★ 2.0k
4
votes
5
replies
3.3k
views
Removing unwanted variation (RUV) for paired analysis ?
ruvseq edger ruvg removebatcheffect
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 10
9
votes
10
replies
15k
views
Is the following a correct usage of Limma's removeBatchEffect() for clustered heat map generation?
limma removeBatchEffect heatmap clustering
updated 9.8 years ago by ▴ 610 • written 9.8 years ago by ▴ 80
20 results • Page 1 of 1
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Replies
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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