Showing : batch • reset
4
votes
7
replies
1.3k
views
DESeq2 one group vs multiple groups comparison in presence of batch effect
deseq2 comparison batch
updated 9 months ago by • 0 • written 2.1 years ago by • 0
0
votes
1
reply
159
views
Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 9 months ago by 3.4k • written 9 months ago by • 0
0
votes
5
replies
392
views
DeSeq2 with three batches - Remove batch Effect
deseq2 batch removebatch effect
updated 11 months ago by 34k • written 11 months ago by ▴ 20
1
vote
4
replies
322
views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA zinbwave batch IntegratedData
updated 12 months ago by ▴ 870 • written 12 months ago by ★ 1.5k
2
votes
8
replies
857
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
13 months ago Pietro ▴ 30
0
votes
2
replies
139
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2 miRNASeq designmatrix Batch
updated 17 months ago by 34k • written 17 months ago by • 0
0
votes
3
replies
264
views
Highly variable gene analysis including RUVs batch correction
deseq2 RUV batch highly variable genes
updated 19 months ago by • 0 • written 19 months ago by • 0
0
votes
1
reply
339
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2 ruv batch
updated 23 months ago by 34k • written 23 months ago by • 0
3
votes
3
replies
285
views
DESeq2 indirect batch effect removal
deseq2 batch
updated 23 months ago by 34k • written 23 months ago by • 0
6
votes
6
replies
448
views
Limma DEG analysis experiment with partial paired design + batch effect
limma paired batch
updated 2.0 years ago by 43k • written 2.0 years ago by ▴ 20
6
votes
18
replies
6.2k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
2.3 years ago Mozart ▴ 20
0
votes
1
reply
288
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 2.4 years ago by 34k • written 2.4 years ago by ▴ 20
3
votes
5
replies
523
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 2.5 years ago by ★ 27k • written 2.5 years ago by ▴ 30
0
votes
3
replies
348
views
DESEQ2 Batch effect
deseq2 batch
updated 2.5 years ago by 34k • written 2.5 years ago by • 0
3
votes
3
replies
500
views
Correcting the batch effect in Edgeseq data
DESeq2 Edgeseq batch
updated 2.7 years ago by 34k • written 2.7 years ago by ▴ 30
0
votes
4
replies
1.4k
views
DESeq2: Outliers, covariates and number of replicates
deseq2 ruvseq cookscutoff covariates batch
4.8 years ago j.viana • 0
2
votes
1
reply
692
views
Does order of removeBatchEffect() and DE subsetting matter for clustered heat map visualization?
rna-seq edgeR limma removebatcheffect() batch
updated 5.6 years ago by ★ 27k • written 5.6 years ago by ▴ 70
17 results • Page 1 of 1
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Answer: Undefined columns error R cytometry analysis by Jiang, Mike ★ 1.3k
I see you are trying to fill the missing transform info to `gs_bcell_auto` , which is a hack, but since you seems to know what you are doin…
Comment: how to get MFI stats from data by Jiang, Mike ★ 1.3k
Can you grant the public caccess to you fcs to reproduce your issue?
Answer: Getting a dataset that only contains the flow data within the gated area by Jiang, Mike ★ 1.3k
You didn't post your example code, so here is my best guess of your workflow > library(flowCore) > library(flowWorkspace) …
Comment: Diffbind dba.plotProfile attempt to select less than one element in OneIndex by bhanratt • 0
``` > DBA 10 Samples, 31953 sites in matrix: ID Tissue Factor Condition Replicate Reads FRiP 1 58 1 H3K4me3 AD …
Answer: Warning messages on Apple M1 BigSur by Vincent J. Carey, Jr. 6.5k
We are not producing M1 binaries at this time. If you use the intel version of R under Rosetta 2 you can use the intel mac binaries.
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Comment: Use of coef() as a measure of effect size in a multiple regression using DESeq2
Answer: Log fold change interpretation of time series with Wald test
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