Showing : limmaGUI • reset
2
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4
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813
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how limma work with continous variables
GordonSmyth limmaGUI lmFit voom
updated 7 months ago by 52k • written 7 months ago by ▴ 40
1
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3
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751
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 11 months ago by 52k • written 11 months ago by • 0
0
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2
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626
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limma model matrix questions
limmaGUI limma pairedsamples
13 months ago whyw6948 • 0
0
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1
reply
507
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Main effect on multiple comparisons in limma
limmaGUI lim MultipleComparison multip
updated 13 months ago by 52k • written 13 months ago by • 0
1
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4
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1.1k
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limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 13 months ago by 52k • written 13 months ago by ▴ 10
1
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5
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1.7k
views
Does voom normalization quantile create difference in DGE genes when distribution of patients is similar (no big differences in quantiles)?
limmaGUI normalization limma voom Normalization
updated 20 months ago by 52k • written 21 months ago by • 0
0
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1
reply
947
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 23 months ago by 52k • written 23 months ago by • 0
1
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1
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1.1k
views
Weird distribution of p-values, with no significant adjusted p-values?
fdr limmaGUI p-values limma
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
1
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2
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1.4k
views
Limma adj.p.value the same for many different p.values
limmaGUI limma adj.p.value StatisticalMethod
2.5 years ago walkerrh95 • 0
2
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6
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1.7k
views
Limma beta coefficient confidence intervals
limma limmaGUI beta
2.7 years ago fluentin44 • 0
0
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1
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1.1k
views
Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
3
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6
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11k
views
Unable to install "limma" package on RStudio
Bioconductor limma limmaGUI
3.1 years ago jaydengitt • 0
6
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4
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1.3k
views
Limma prametrization
limm MathematicalBiology limmaGUI StatisticalMethod
3.2 years ago Giovanni • 0
0
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1
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1.8k
views
shiny account on mac not deploying server
limmagui shiny
9.0 years ago christopher.clarskon15 ▴ 20
2
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5
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2.2k
views
NA coefficients values for samples with all zeros
limmagui proteomics
9.3 years ago vedran.franke • 0
1
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5
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3.5k
views
Using Limma for proteomics (2D DIGE) datasets
Proteomics limma impute limmaGUI Proteomics limma impute limmaGUI
updated 9.7 years ago by • 0 • written 15.4 years ago by ▴ 60
0
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0
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1.4k
views
ATTN: Clark Wilson filtering for present calls
limmaGUI limmaGUI
14.9 years ago Sinha, Mala ▴ 10
0
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2
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1.4k
views
problem detected during utilization of LimmaGUI
Microarray limmaGUI Microarray limmaGUI
updated 15.3 years ago by ★ 7.4k • written 15.3 years ago by ▴ 10
0
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4
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1.7k
views
getting normexp (and log2 transformed) values - not further-processed M values
Microarray limma limmaGUI Microarray limma limmaGUI
15.5 years ago adoty@umd.edu ▴ 30
0
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1
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1.4k
views
limmaGUI - venn-diagram & top-table anomaly?
limmaGUI limmaGUI
updated 15.6 years ago by ▴ 450 • written 15.6 years ago by ▴ 10
0
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0
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1.1k
views
exclude spots with zero weight 0 from lmfit toptable list in limmaGUI
Normalization limma limmaGUI Normalization limma limmaGUI
16.3 years ago Christine Voellenkle ▴ 90
0
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1
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1.8k
views
statistics for differential expression: adjusted p-values<0.05 BUT negative B-odds?
Normalization limma limmaGUI Normalization limma limmaGUI
updated 16.4 years ago by ▴ 320 • written 16.4 years ago by ▴ 90
0
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1
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1.4k
views
asMatrixWeights: weights of unexpected shape
GUI limma limmaGUI GUI limma limmaGUI
updated 16.5 years ago by ▴ 90 • written 16.5 years ago by 52k
0
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3
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1.6k
views
duplicate correlation of 4 "within array replicates" limmaGUI
GUI limma limmaGUI microRNA GUI limma limmaGUI microRNA
16.5 years ago Gordon Smyth 52k
0
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2
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2.5k
views
problem with tkrplot installation
limmaGUI limmaGUI
updated 16.6 years ago by 68k • written 16.6 years ago by ▴ 20
0
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6
replies
2.6k
views
Is anyone developing an extensible Galaxy-like interface for Bioconductor?
affylmGUI limmaGUI affylmGUI limmaGUI
updated 16.6 years ago by ▴ 10 • written 16.7 years ago by ▴ 50
0
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2
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1.7k
views
Is anyone developing an extensible Galaxy-like interface for Bioconductor?
affylmGUI limmaGUI affylmGUI limmaGUI
updated 16.6 years ago by ▴ 90 • written 16.6 years ago by ▴ 140
0
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0
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1.1k
views
Is anyone developing an extensible Galaxy-like interface for Bioconductor?
Cancer affylmGUI limmaGUI Cancer affylmGUI limmaGUI
16.7 years ago Martin Morgan 25k
0
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2
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1.4k
views
limmaGUI: target file and spot file
limmaGUI limmaGUI
updated 16.7 years ago by ▴ 910 • written 16.7 years ago by ▴ 10
0
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0
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1.3k
views
error asMatrixWeights in LimmaGUI
Microarray limmaGUI Microarray limmaGUI
16.7 years ago bzzandrew@interfree.it ▴ 30
0
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1
reply
2.3k
views
Limma user’s guide example data sets
Microarray limma limmaGUI weaver Microarray limma limmaGUI weaver
updated 16.8 years ago by ▴ 130 • written 16.8 years ago by ▴ 450
0
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1
reply
1.5k
views
One-Color Agilent Data into Limma GUI
GO limma limmaGUI GO limma limmaGUI
updated 17.5 years ago by ★ 1.9k • written 17.5 years ago by ▴ 230
0
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2
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1.4k
views
help for limmaGUI
Microarray limmaGUI Microarray limmaGUI
updated 17.8 years ago by ★ 1.9k • written 17.8 years ago by ▴ 10
0
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3
replies
1.6k
views
limma: print-tip loess and empty spots
Normalization GO GUI limma limmaGUI Normalization GO GUI limma limmaGUI
17.8 years ago Gordon Smyth 52k
0
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0
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3.0k
views
Tcl/TK package "Bwidget" when using limmaGUI or affylmGUI
limmaGUI affylmGUI
updated 7 months ago by 52k • written 17.9 years ago by ▴ 450
0
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1
reply
1.3k
views
[Bioc] Tcl/TK pckage "Bwidget"
limmaGUI limmaGUI
updated 17.9 years ago by ▴ 10 • written 17.9 years ago by 21k
0
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0
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1.1k
views
Duplicated spots in limmaGUI
limmaGUI limmaGUI
17.9 years ago Gordon Smyth 52k
0
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1
reply
1.4k
views
Duplicated spots in limmaGUI
limmaGUI limmaGUI
updated 17.9 years ago by ▴ 500 • written 17.9 years ago by ▴ 80
0
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1
reply
1.2k
views
Limma - Design related problem: Unconnected design and time-treatment interaction estimation
Microarray Cancer limma limmaGUI Microarray Cancer limma limmaGUI
updated 18.1 years ago by ★ 6.0k • written 18.1 years ago by ▴ 90
0
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0
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1.4k
views
Computing a diference of 2 differences from a CpG Island experiment using LimmaGUI
Cancer limmaGUI Cancer limmaGUI
18.4 years ago Darlene Goldstein ▴ 230
0
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0
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1.2k
views
limma citations [was LimmaGUI for illumina data]
Annotation GUI Kidney limma affylmGUI limmaGUI Annotation GUI Kidney limma affylmGUI
18.8 years ago Gordon Smyth 52k
0
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0
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1.2k
views
LimmaGUI for illumina data
GUI affy limma affylmGUI limmaGUI beadarray GUI affy limma affylmGUI limmaGUI beadarray
18.8 years ago Mark Dunning ▴ 320
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0
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1.1k
views
LimmaGUI for illumina data
GUI limma affylmGUI limmaGUI GUI limma affylmGUI limmaGUI
18.8 years ago Roy Williams ▴ 10
0
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1
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1.4k
views
reference design
limma limmaGUI oligo limma limmaGUI oligo
updated 18.9 years ago by ★ 6.0k • written 18.9 years ago by ▴ 30
0
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0
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1.4k
views
parameterization or contrast matrix?
limma limmaGUI oligo limma limmaGUI oligo
18.9 years ago bzzandrew@interfree.it ▴ 30
0
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3
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2.3k
views
Limma: correct calculation of B statistics (log odds)
limma limmaGUI limma limmaGUI
updated 18.9 years ago by ▴ 290 • written 18.9 years ago by ★ 1.9k
1
vote
3
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4.1k
views
Limma: correct calculation of B statistics (log odds)
Microarray Genetics limma limmaGUI Microarray Genetics limma limmaGUI
updated 18.9 years ago by ★ 1.9k • written 18.9 years ago by 52k
0
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1
reply
1.1k
views
Different results Limma vs LimmaGUI?
limma limmaGUI limma limmaGUI
updated 19.0 years ago by ★ 1.9k • written 19.0 years ago by 52k
0
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0
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1.0k
views
Different results Limma vs LimmaGUI?
limma limmaGUI limma limmaGUI
19.0 years ago J.delasHeras@ed.ac.uk ★ 1.9k
0
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3
replies
2.6k
views
Limma: background correction. Use or ignore?
Microarray Cancer affy limma limmaGUI Microarray Cancer affy limma limmaGUI
updated 19.0 years ago by ★ 1.9k • written 19.0 years ago by 52k
50 results • Page 1 of 1
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Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20
I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…
Answer: Error in cnetplot by Guido Hooiveld ★ 4.1k
Unfortunately you did not show how you generated your input data (the object `enrichment`), nor did you show the output from `sessionInfo()…
Answer: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
I think this is because Ensembl can assign different Gene IDs to "the same gene" if it is found both on a standard chromosome and a scaffol…
Votes
Answer: Explannation for ROAST results
Comment: Limma comparing gene expression between base line and one treatment
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
clusterProfiler-GO enrichment Error
A: Machine learning in R book
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