Showing : VOOM • reset
2
votes
9
replies
234
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
9 days ago • updated 4 days ago Peipei • 0
2
votes
2
replies
139
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 6 weeks ago by 45k • written 6 weeks ago by ▴ 10
1
vote
4
replies
288
views
Limma: How to deal with multiple batch effects and what is going on under the hood
limma voom
updated 8 weeks ago by 45k • written 9 weeks ago by ▴ 10
0
votes
3
replies
230
views
limma voom contrasts
contrasts limma voom
updated 3 months ago by 45k • written 3 months ago by ▴ 80
0
votes
3
replies
290
views
Need help with a contrast design for limma with a missing group?
limma VOOM
updated 4 months ago by 45k • written 4 months ago by ▴ 50
2
votes
5
replies
581
views
limma-trend and voom results do not agree
limma limma-trend voom RNASeq
7 months ago • updated 6 months ago Tyler Sagendorf • 0
3
votes
2
replies
380
views
Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
7 months ago altintas.ali • 0
0
votes
2
replies
421
views
Mean-variance trend and identifying significant DE with large amount of biological change in expression in time-series data
voom
7 months ago • updated 6 months ago hmviit • 0
0
votes
2
replies
394
views
voom flips the sign relative to log(cpm)
limma limma-voom rnaseq voom
updated 9 months ago by 45k • written 9 months ago by • 0
0
votes
1
reply
384
views
limma/voom for protein intensity data
limma proteomics voom
updated 9 months ago by ★ 1.3k • written 9 months ago by ▴ 60
0
votes
2
replies
353
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
10 months ago James • 0
0
votes
2
replies
366
views
voom-limma workflow for RNAseq samples with very different numbers of counts
voom limma RNASeq
15 months ago annadv • 0
0
votes
2
replies
1.1k
views
TPM data in limma/voom
voom limma DifferentialExpression edgeR
16 months ago RJM • 0
1
vote
1
reply
663
views
Limma-Voom - Time series experiment with one group (duplicateCorrelation() function)
voom duplicateCorrelation() timeseries limma
updated 18 months ago by 45k • written 18 months ago by ▴ 10
6
votes
13
replies
1.7k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 22 months ago by 45k • written 22 months ago by ▴ 50
0
votes
5
replies
520
views
isoform data, deep sequencing and voom
isoform deep sequencing voom
updated 22 months ago by 45k • written 22 months ago by ▴ 620
0
votes
4
replies
391
views
mean-variance trend plots with isoform and gene-level data from tximport
tximport isoform voom
updated 23 months ago by 45k • written 23 months ago by ▴ 620
1
vote
4
replies
376
views
How to compare a single RNA-Seq sample with microarray samples?
voom rna-seq microarray
updated 2.0 years ago by 60k • written 2.0 years ago by ▴ 10
0
votes
1
reply
302
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 2.0 years ago by 45k • written 2.0 years ago by • 0
2
votes
6
replies
617
views
linear mixed models using edgeR+limma
linear mixed model edger limma voom RNA-seq
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
1
vote
5
replies
482
views
Limma for proteomic data! Please Help!
limma voom lmfit ebayesfit
updated 2.2 years ago by 45k • written 2.2 years ago by • 0
0
votes
2
replies
224
views
estimating variability in absence of replicates for edgeR
edgeR RNAseq voom variability estimator
updated 2.3 years ago by 45k • written 2.3 years ago by • 0
2
votes
6
replies
475
views
paired and unpaired test at the same time with voom limma
limma voom rna-seq paired test unpaired test
updated 2.3 years ago by 45k • written 2.3 years ago by • 0
6
votes
5
replies
778
views
How to know if I should use voomWithQualityWeights() or not?
limma RNA-Seq voom voomWithQualityWeights edgeR
updated 2.3 years ago by 45k • written 2.3 years ago by • 0
0
votes
0
replies
282
views
RNAseq/miRNAseq normalization for calculating gene correlations, survival analysis, and exploratory graphing
limma edger voom rnaseq mirnaseq
2.4 years ago atakanekiz ▴ 30
4
votes
7
replies
675
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 50
3
votes
6
replies
1.3k
views
Understanding voom behavior when model matrix is used with/without intercept for a continuous variable
limma voom rnaseq model.matrix intercept
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 30
0
votes
0
replies
342
views
limma-voom group design and its effect on sva
limma voom group-design sva
2.6 years ago kentfung • 0
2
votes
4
replies
628
views
Limma gives big p-values for large LFC
limma voom
updated 2.7 years ago by 45k • written 2.7 years ago by • 0
4
votes
5
replies
507
views
Defining the design for a complicated multi-level experiment in Limma
limma RNASeq R voom
updated 2.7 years ago by 60k • written 2.7 years ago by ▴ 20
0
votes
1
reply
614
views
Variance unstable after fitting to linear model with limma-voom pipeline
limma voom
2.7 years ago kentfung • 0
4
votes
3
replies
849
views
Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancePartition dream
updated 2.7 years ago by ▴ 90 • written 3.0 years ago by ▴ 50
0
votes
3
replies
372
views
Design matrix for cohort with samples outside "block"
limma voom sva
2.9 years ago kentfung • 0
0
votes
3
replies
426
views
How to apply a linear mixed model onto an RNA-Seq data?
limma linear mixed model voom rna-seq
2.9 years ago Assa Yeroslaviz ★ 1.5k
4
votes
4
replies
495
views
normalization of RNA-seq data after over-expressing the transcription factors
limma deseq2 voom edgeR
updated 2.9 years ago by ★ 27k • written 2.9 years ago by ▴ 640
3
votes
4
replies
1.1k
views
MDS plotting within the limma/voom workflow
limma voom deseq2
updated 3.0 years ago by 45k • written 3.0 years ago by ▴ 50
1
vote
5
replies
577
views
Time course experiment using limma with voom
limma voom RNA Seq Time-course experiments
updated 3.0 years ago by ★ 27k • written 3.0 years ago by • 0
2
votes
2
replies
492
views
voomWithQualityWeights together with covariate in design matrix
limma voom RNA-seq voomWithQualityWeights
updated 3.1 years ago by ▴ 1000 • written 3.1 years ago by ▴ 90
1
vote
2
replies
499
views
Why does limma voom E value give different result than the voom object
limma voom rna-seq
updated 3.1 years ago by ▴ 160 • written 3.1 years ago by ▴ 50
5
votes
7
replies
1.1k
views
limma - blocking or regressing out nuisance variable
limma voom RNA-seq
updated 3.2 years ago by 60k • written 3.2 years ago by ▴ 20
0
votes
3
replies
650
views
~50% significant genes from RNA (NanoString) Differential Expression Analysis
limma microarray voom
3.3 years ago rueben.bautista7 • 0
7
votes
3
replies
2.0k
views
VOOM vs VSN vs log2 to transform proteome data before LIMMA analysis
r limma voom vsn
updated 3.3 years ago by 13k • written 3.3 years ago by ▴ 70
12
votes
4
replies
3.3k
views
differential expression analysis of htseq data with edgeR/voom
voom htseq edgeR limma RNASeq123
updated 3.5 years ago by 45k • written 5.1 years ago by ▴ 30
2
votes
2
replies
595
views
Different results from limma depending on whether or not I have an intercept term in my model
limma lmfit voom limma design matrix voomwithqualityweights
updated 3.5 years ago by 45k • written 3.5 years ago by ▴ 10
5
votes
5
replies
879
views
t-statistic from various limma-approaches does not follow the theoretical distribution
limma t-statistic voom voomwithqualityweights robust regression
3.6 years ago brynedal ▴ 30
3
votes
6
replies
1.2k
views
Controlling numerical covariates: differential gene expression with limma voom
limma voom differential gene expression rnaseq R
updated 3.6 years ago by ▴ 260 • written 3.6 years ago by • 0
2
votes
4
replies
789
views
Inconsistent result between limma/voom and DESeq2
deseq2 limma voom limma-voom rnaseq
updated 3.6 years ago by 45k • written 3.6 years ago by ▴ 40
5
votes
4
replies
786
views
Limma Voom duplicateCorrelation Design
limma voom duplicatecorrelation
updated 3.6 years ago by ★ 27k • written 3.6 years ago by ▴ 30
2
votes
2
replies
718
views
voom variance modeling: lowess curve fitting notation misunderstanding?
voom
updated 3.6 years ago by 45k • written 3.6 years ago by • 0
8
votes
8
replies
3.7k
views
Voom transformation from counts and normalization to negative values
rnaseq voom limma tcga statistics
updated 3.8 years ago by 7.8k • written 3.8 years ago by ▴ 50
50 results • Page 1 of 1
Recent ...
Replies
Comment: Using Age or other numerical variable to model expression in deseq2 by krushnach80 • 0
"Why is that" no as an example i was citing that.."certainly don't want to make the interaction between the nuisance variable and your vari…
Comment: Using Age or other numerical variable to model expression in deseq2 by James W. MacDonald 60k
You have to use age from that post? Why is that? It is rarely optimal to categorize age rather than use as a continuous variable. It takes …
Comment: Using Age or other numerical variable to model expression in deseq2 by krushnach80 • 0
if I have to use age from this [post][1] i think this is more cleaner way to make group or make category of age groups [1]: https://su…
Comment: Using Age or other numerical variable to model expression in deseq2 by krushnach80 • 0
I know the result but i was not clear about the interpretation because if i use that numerical variable which is turned into factor for exa…
Comment: I got error message about DESeqDataSetFromMatrix by swbarnes2 ★ 1.1k
Well, what do you think the error means based on what it says?
Votes
Comment: Using Age or other numerical variable to model expression in deseq2
Comment: Using Age or other numerical variable to model expression in deseq2
Answer: Using Age or other numerical variable to model expression in deseq2
Answer: Using Age or other numerical variable to model expression in deseq2
Answer: Trouble importing my own Gene Ontology Annotation into topGO
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