Showing : limma • reset
2
votes
5
replies
104
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2 Transcriptomics Visualization R limma
updated 12 hours ago by 45k • written 2 days ago by ▴ 10
3
votes
4
replies
91
views
Quantile Normalization after rma or not?
limma Microarray oligo
1 day ago Yang Shi • 0
2
votes
2
replies
88
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 5 days ago by 45k • written 5 days ago by ▴ 10
1
vote
2
replies
76
views
toptable sort .by set
limma rnaseqGene
7 days ago snowmattin • 0
1
vote
5
replies
171
views
Unsuccessful DE analysis using limma - voom
limma
9 days ago • updated 8 days ago loainaom • 0
2
votes
1
reply
81
views
Extremely low P-values when using Limma on high sample size proteomics data
limma Proteomics
updated 9 days ago by 59k • written 9 days ago by • 0
2
votes
1
reply
64
views
Limma model orientation
limma methylation MethylationArray
updated 14 days ago by 59k • written 15 days ago by • 0
2
votes
4
replies
145
views
Overfitting in limma
limma Regression overfitting
updated 8 days ago by 45k • written 15 days ago by • 0
0
votes
0
replies
56
views
diffcyt - topTable function returns one total significance estimate instead of one per comparison
limma diffcyt edgeR
20 days ago stefanos.bamopoulos • 0
1
vote
4
replies
224
views
Limma: How to deal with multiple batch effects and what is going on under the hood
limma voom
updated 22 days ago by 45k • written 24 days ago by ▴ 10
0
votes
3
replies
101
views
Limma time course with several conditions
limma
23 days ago • updated 22 days ago rina ▴ 20
0
votes
7
replies
275
views
Which Limma guide is recommended ?
limma R DifferentialExpression
4 weeks ago • updated 16 days ago loainaom • 0
0
votes
2
replies
148
views
Time course experiment using limma
limma Multi-levelExperiments Microarray
4 weeks ago Wendy • 0
3
votes
4
replies
206
views
How to make design matrices or compare contrast in limma
designmatrices differentialexpression makeContrasts limma model.matrix
5 weeks ago mohammedtoufiq91 ▴ 10
2
votes
2
replies
162
views
Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
6 weeks ago • updated 5 weeks ago fluentin44 • 0
1
vote
6
replies
240
views
Differential expression analysis - Clariom S array -workflow
design-matrix limma
6 weeks ago ala • 0
0
votes
1
reply
1.0k
views
Three questions about processing Agilent Arrays
Normalization limma PROcess Normalization limma PROcess
updated 6 weeks ago by 45k • written 13.2 years ago by ▴ 30
0
votes
1
reply
122
views
Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 6 weeks ago by 36k • written 6 weeks ago by • 0
1
vote
4
replies
190
views
lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
7 weeks ago sushimoto • 0
1
vote
3
replies
154
views
how to change axis labeling in limma density plot
desnity limma
updated 7 weeks ago by 45k • written 7 weeks ago by ▴ 10
0
votes
4
replies
227
views
How to model a pre and post treatment in limma
limma
7 weeks ago AST ▴ 50
0
votes
10
replies
1.1k
views
Limma : time course experiment with missing data
limma limma-voom
written 4.2 years ago by • 0
0
votes
4
replies
222
views
limma: Genes Associated with Continuous Predictor in Subsets of Samples
RNASeq limma
8 weeks ago • updated 7 weeks ago danphillips28 • 0
0
votes
0
replies
117
views
Differences between limma and edgeR
limma
9 weeks ago • updated 8 weeks ago jose.carmeliet • 0
6
votes
2
replies
162
views
The number of controls versus treatment in differential expression analysis
DESeq2 edgeR limma
updated 8 weeks ago by 45k • written 9 weeks ago by ▴ 30
4
votes
2
replies
151
views
Covariates to be included in DE model
DESeq2 limma
updated 9 weeks ago by 45k • written 9 weeks ago by • 0
0
votes
9
replies
326
views
Handling of missing values in limma
limma missingValues
updated 1 day ago by 45k • written 9 weeks ago by • 0
0
votes
1
reply
157
views
Limma interaction term
RNASeqData limma DifferentialExpression
updated 10 weeks ago by 45k • written 10 weeks ago by • 0
2
votes
2
replies
180
views
Complex contrasts in limma
RNASeq limma DifferentialExpression
10 weeks ago tcalvo ▴ 70
0
votes
6
replies
391
views
how plotSA shall look like for good or bad data, any example of good or bad data shall look like in plotSA regarding whether the data is OK for limma…
plotSA limma
11 weeks ago • updated 10 weeks ago Ming ▴ 360
0
votes
3
replies
192
views
limma voom contrasts
contrasts limma voom
updated 10 weeks ago by 45k • written 11 weeks ago by ▴ 80
2
votes
3
replies
210
views
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
11 weeks ago nhaus • 0
0
votes
3
replies
259
views
Need help with a contrast design for limma with a missing group?
limma VOOM
updated 12 weeks ago by 45k • written 12 weeks ago by ▴ 50
2
votes
1
reply
189
views
DESeq2 handling of replicates
DESeq2 RNASeq limma
updated 12 weeks ago by 36k • written 12 weeks ago by • 0
1
vote
1
reply
176
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 12 weeks ago by ★ 1.2k • written 12 weeks ago by • 0
0
votes
1
reply
189
views
Running limma in parallel
parallel R limma EWAS
updated 12 weeks ago by 45k • written 12 weeks ago by • 0
3
votes
6
replies
463
views
Unable to install "limma" package on RStudio
Bioconductor limma limmaGUI
3 months ago • updated 12 weeks ago jaydengitt • 0
4
votes
5
replies
373
views
What to do if covariates in design matrix of limma are confounded
limma DifferentialExpression
updated 17 days ago by • 0 • written 12 weeks ago by • 0
5
votes
5
replies
309
views
Where to find old limma packages not part of a Bioc release?
archive limma
3 months ago Jonathan • 0
0
votes
1
reply
171
views
How to design limma for two populations from each tumor, multiple tumors from several of the patients
limma
updated 3 months ago by 45k • written 3 months ago by • 0
0
votes
2
replies
258
views
Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 3 months ago by 45k • written 3 months ago by • 0
0
votes
4
replies
330
views
How do you get averages of each group in Limma output
RNASeq limma
3 months ago Matthew • 0
4
votes
3
replies
296
views
Limma/voom analysis of time-series data (with only 1 condition)
limma DifferentialExpression
updated 3 months ago by 59k • written 3 months ago by • 0
1
vote
4
replies
291
views
Phosphoproteomics time series analysis with splines
limma splines
4 months ago rina ▴ 20
1
vote
1
reply
410
views
Error in rowMeans(y$exprs, na.rm = TRUE) : 'x' must be numeric
limma
updated 4 months ago by 45k • written 4 months ago by • 0
0
votes
0
replies
126
views
Complex design in DESeq2 doesn't seem to be supported in Glimma
limma Glimma RNASeq DESeq2
4 months ago Jonas • 0
2
votes
2
replies
948
views
EdgeR installation issue
limma edgeR DESeq2
4 months ago aonghus • 0
2
votes
5
replies
511
views
Adjust for base line gene expression in limma model
limma Microarray
updated 4 months ago by 45k • written 5 months ago by • 0
0
votes
2
replies
225
views
Filtering low coverage RRBS counts results in few reads. Any alternatives?
limma edgeR
updated 5 months ago by • 0 • written 5 months ago by • 0
2
votes
5
replies
521
views
limma-trend and voom results do not agree
limma limma-trend voom RNASeq
6 months ago • updated 5 months ago Tyler Sagendorf • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: ashr vs apeglm for interaction data by Michael Love 36k
Can you show the MA plot for these two analyses? Also for a gene with a large LFC from ashr, can you show plotCounts?
Comment: Robust Multi-array Average could get negative value or not? by Yang Shi • 0
Got the point sir~ Thanks so much!
Comment: Robust Multi-array Average could get negative value or not? by James W. MacDonald 59k
Because it's a small number.
Comment: Robust Multi-array Average could get negative value or not? by Yang Shi • 0
Thanks for your quick reply sir! Could you tell me why 4 which you selected here?
Answer: Robust Multi-array Average could get negative value or not? by James W. MacDonald 59k
After running RMA, your data have been logged, base 2. Any value < 1 will have a negative value. Looking at the data from that GEO submissi…
Votes
Answer: Robust Multi-array Average could get negative value or not?
Answer: Robust Multi-array Average could get negative value or not?
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
Awards • All
Scholar to James W. MacDonald 59k
Scholar to Guido Hooiveld ★ 3.2k
Scholar to Kevin Blighe 3.5k
Scholar to SamGG ▴ 270
Prophet to johnmcma ▴ 10
Locations • All
United Kingdom, 1 minute ago
United States, 2 minutes ago
United States, 3 minutes ago
Zheng Zhou, 4 minutes ago
United Kingdom, 6 minutes ago
Traffic: 513 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6