Showing : EDGER • reset
0
votes
2
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1.3k
views
Normalization and dispersion estimates in timeseries data with highly variable read numbers
EdgeR dispersion normalization
updated 5.7 years ago by 53k • written 5.7 years ago by • 0
3
votes
6
replies
4.6k
views
Including multiple covariates in edgeR
edger R limma
updated 5.7 years ago by 53k • written 5.7 years ago by • 0
0
votes
1
reply
675
views
Mathematical View of Timmer Mean of M-values
edgeR
updated 5.7 years ago by 53k • written 5.7 years ago by • 0
1
vote
3
replies
1.7k
views
EdgeR - How to define a group when calculating BCV
edgeR
updated 5.7 years ago by ▴ 900 • written 5.7 years ago by • 0
0
votes
0
replies
1.2k
views
RNAseq/miRNAseq normalization for calculating gene correlations, survival analysis, and exploratory graphing
limma edger voom rnaseq mirnaseq
5.7 years ago atakanekiz ▴ 30
1
vote
2
replies
1.7k
views
Problem with readDGE
edger
updated 5.7 years ago by 53k • written 5.7 years ago by • 0
1
vote
5
replies
1.8k
views
edgeR - design matrix and contrasts for paired data problems
edger
5.8 years ago • updated 5.7 years ago emelie.nilsson • 0
1
vote
3
replies
1.6k
views
TMM normalisation on metatranscriptome data: for visualisation/fold-change only
normalization edgeR metatranscriptome
updated 5.8 years ago by 53k • written 5.8 years ago by • 0
2
votes
4
replies
3.0k
views
edgeR design matrix and contrasts for comparisons both between and within subjects
edger rnaseq design and contrast matrix
updated 5.8 years ago by 53k • written 5.8 years ago by • 0
3
votes
2
replies
3.7k
views
How to deal with elimination of genes when using filterByExpr function?
edger DEGs normalization
updated 5.8 years ago by 53k • written 5.8 years ago by ▴ 10
0
votes
3
replies
1.0k
views
Cannot figure out why the DE genes' FDR > 0.05 in edgeR output
edger rnaseq
updated 5.8 years ago by 53k • written 5.8 years ago by • 0
2
votes
4
replies
1.4k
views
How to make grouping and contrast for multfactor design?
edger DEGs
5.8 years ago anikng ▴ 10
6
votes
11
replies
3.1k
views
Correct use of tximport in combination with edgeR cpm()
tximport edgeR
6.5 years ago • updated 5.8 years ago ATpoint ★ 5.0k
4
votes
8
replies
1.8k
views
problem in designing matrix and batch effect
edger rna-seq matrix
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
0
votes
2
replies
521
views
Sequencing machine as fixed effect in DEseq2?
deseq2 edger
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
2
replies
897
views
How to perform multiple comparisons with no biological replication using edgeR
edgeR no replication glmLRT(fit coef=2)
updated 5.9 years ago by 53k • written 5.9 years ago by • 0
2
votes
2
replies
6.0k
views
understanding edgeR glmLRT
edger lrt
updated 5.9 years ago by 53k • written 5.9 years ago by • 0
3
votes
8
replies
1.9k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
4
votes
7
replies
2.3k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 5.9 years ago by 53k • written 5.9 years ago by ▴ 60
0
votes
2
replies
1.2k
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2 design formula design matrix edgeR ATAC
updated 5.9 years ago by 53k • written 5.9 years ago by • 0
0
votes
0
replies
999
views
EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
5.9 years ago ingerslev • 0
0
votes
0
replies
1.0k
views
cqn vignette error
cqn normalization edger
5.9 years ago Jenny Drnevich ★ 2.0k
1
vote
1
reply
1.0k
views
Normalized counts access in DESeq2 R: with and without batch
deseq2 edger normalization
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 60
2
votes
5
replies
1.5k
views
Nested Random Effect in LIMMA: Is It Possible?
limma rna-seq edger random effects
updated 5.9 years ago by 53k • written 5.9 years ago by • 0
2
votes
1
reply
942
views
Detecting the power in differential expression
POWER DESEQ2 edger LIMMA DIfferential expression
6.0 years ago • updated 5.9 years ago Beginner • 0
1
vote
4
replies
1.3k
views
Difference between Fold Changes from EdgeR glmLRTest and directly calculated fold changes.
edger RNA Seq
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 30
2
votes
2
replies
2.1k
views
"filterByExpr" Function filtered out all my counts
edger
updated 6.0 years ago by 53k • written 6.0 years ago by ▴ 20
3
votes
7
replies
1.6k
views
edgeR lable shuffling permutation test
edger
updated 6.0 years ago by 53k • written 6.0 years ago by • 0
1
vote
7
replies
3.7k
views
EdgeR RNAseq -- best way to deal with random effects
edger rnaseq
updated 6.0 years ago by • 0 • written 7.0 years ago by • 0
5
votes
8
replies
3.1k
views
adding "symbol" column in my differential expressed genes in EdgeR
EdgeR
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
5
votes
5
replies
2.8k
views
interpreting FC values from glmTreat, especially unshrunk log-fold-changes
edgeR glmTreat significance testing
updated 6.0 years ago by ▴ 900 • written 6.0 years ago by • 0
2
votes
6
replies
5.5k
views
removing genes before RNA-seq normalization
edger deseq2 normalization removing genes
updated 3.5 years ago by 53k • written 6.0 years ago by ▴ 90
3
votes
2
replies
2.4k
views
Filtering lowly-expressed genes in a RNASeq dataset with continuous instead of grouping variables
limma edger
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
3
votes
3
replies
1.1k
views
Nested Interaction in edgeR and composition bias
edger rna-seq
updated 6.0 years ago by 53k • written 6.0 years ago by • 0
1
vote
5
replies
1.8k
views
edgeR or DESeq2 between duplicated chromosomes in the same individual
deseq2 edgeR normalization DGE
updated 6.0 years ago by 53k • written 6.0 years ago by ▴ 10
3
votes
1
reply
843
views
Account for inter individual variability at the baseline using nested models
limma edger
updated 6.0 years ago by 53k • written 6.0 years ago by • 0
5
votes
3
replies
1.1k
views
EdgeR DGElist - equal counts between treatment and control incorrectly give significant PValue using estimateGLMCommonDisp through DGElist
edger
updated 6.0 years ago by 53k • written 6.0 years ago by ▴ 10
2
votes
4
replies
881
views
Very variable samples vs similar samples in the same dataset
edger deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
2
votes
6
replies
2.2k
views
"adding gene annotations" in edgeR doesn't work with select()
edgeR DEG
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
6
votes
7
replies
3.6k
views
edgeR time series analysis with no replicates
edger
updated 6.1 years ago by • 0 • written 10.1 years ago by ▴ 10
3
votes
6
replies
3.0k
views
Repeated measures per individual and unbalanced number of measures per individual: DE between groups still an ordinary two-group comparison?
differentialexpression deseq2 limma edger repeatedmeasures
6.1 years ago • updated 3.8 years ago hermidalc ▴ 20
3
votes
4
replies
1.2k
views
DESeq2 VS edgeR DEG results different in analysis same data
DESeq2 edgeR
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 10
9
votes
2
replies
1.9k
views
Bug in estimateDisp of "edgeR"? "weights' matched by multiple actual arguments
edger estimateDisp
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 30
9
votes
4
replies
3.2k
views
Does edgeR need to specify reference group?
edgeR reference group
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 10
0
votes
1
reply
395
views
Variation in the estimation of the common dispersion
edger common dispersion
updated 6.1 years ago by 53k • written 6.1 years ago by • 0
8
votes
2
replies
4.2k
views
RNASeq DE analysis starts from different DESeq2 normalized data, TMM normalized data and CPM
limma edger
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 10
3
votes
4
replies
1.8k
views
How to normalize RNA-seq data if majority of transcripts expected to be differentially expressed vs control condition?
rnaseq edger
updated 6.1 years ago by 53k • written 6.1 years ago by • 0
2
votes
2
replies
654
views
Order of design matrix for edgeR analysis
edger r
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
2
votes
7
replies
1.4k
views
Applying norm.factors in RNA-seq analysis to other expression data by using edgeR
edger
updated 6.1 years ago by 53k • written 6.1 years ago by • 0
7
votes
5
replies
2.5k
views
EdgeR - Complex design - contrasts/coefficients
edger GLM
updated 6.1 years ago by ▴ 900 • written 6.1 years ago by ▴ 10
2,031 results • Page 11 of 41
Recent ...
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Comment: After running samtools, the featureCounts command crashed. by eja.gssssse.r.m • 0
The buffer overflow detected error in your featureCount step usually indicates that the program is trying to write more data into memory …
Comment: gene Set with high AUC score but no cells assigned to cell type by eja.gssssse.r.m • 0
It sounds like your AUCell results may be showing high AUC scores without cell assignment due to thresholding or scoring cutoffs. Think of …
Answer: "Watched Tags" are being erased rather than updated by shepherl 4.2k
This should now be resolved
Answer: Question about collapsing ASVs by genus level during DESeq2 analysis by Michael Love 43k
I'll just note that microbiome stats folks tend to use other tools than DESeq2. > several ASVs belong to the same genus but are not iden…
Comment: Integration: Paired-end vs healthy single-end from a different source by igkryycpinmshzugby • 0
Yes, Option 1 (technical homogenization) reprocessing paired-end samples as single-end using only R1 is the most defensible approach when l…
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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