Showing : limmaGUI • reset
2
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4
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710
views
how limma work with continous variables
GordonSmyth limmaGUI lmFit voom
updated 4 months ago by 52k • written 4 months ago by ▴ 40
1
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3
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652
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 8 months ago by 52k • written 8 months ago by • 0
0
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2
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543
views
limma model matrix questions
limmaGUI limma pairedsamples
10 months ago whyw6948 • 0
0
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1
reply
449
views
Main effect on multiple comparisons in limma
limmaGUI lim MultipleComparison multip
updated 10 months ago by 52k • written 10 months ago by • 0
1
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4
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924
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 10 months ago by 52k • written 10 months ago by ▴ 10
1
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5
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1.5k
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 17 months ago by 52k • written 17 months ago by • 0
0
votes
1
reply
869
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 19 months ago by 52k • written 20 months ago by • 0
1
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1
reply
1.0k
views
Weird distribution of p-values, with no significant adjusted p-values?
fdr limmaGUI p-values limma
updated 2.2 years ago by 67k • written 2.2 years ago by • 0
1
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2
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1.3k
views
Limma adj.p.value the same for many different p.values
limmaGUI limma adj.p.value StatisticalMethod
2.2 years ago walkerrh95 • 0
2
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6
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1.5k
views
Limma beta coefficient confidence intervals
limma limmaGUI beta
2.5 years ago fluentin44 • 0
0
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1
reply
987
views
Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
3
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6
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9.5k
views
Unable to install "limma" package on RStudio
Bioconductor limma limmaGUI
2.8 years ago jaydengitt • 0
6
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4
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1.2k
views
Limma prametrization
limm MathematicalBiology limmaGUI StatisticalMethod
2.9 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
8.7 years ago christopher.clarskon15 ▴ 20
2
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5
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2.0k
views
NA coefficients values for samples with all zeros
limmagui proteomics
9.1 years ago vedran.franke • 0
1
vote
5
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3.3k
views
Using Limma for proteomics (2D DIGE) datasets
Proteomics limma impute limmaGUI Proteomics limma impute limmaGUI
updated 9.5 years ago by • 0 • written 15.2 years ago by ▴ 60
0
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0
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1.3k
views
ATTN: Clark Wilson filtering for present calls
limmaGUI limmaGUI
14.7 years ago Sinha, Mala ▴ 10
0
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2
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1.3k
views
problem detected during utilization of LimmaGUI
Microarray limmaGUI Microarray limmaGUI
updated 15.0 years ago by ★ 7.4k • written 15.0 years ago by ▴ 10
0
votes
4
replies
1.6k
views
getting normexp (and log2 transformed) values - not further-processed M values
Microarray limma limmaGUI Microarray limma limmaGUI
15.2 years ago adoty@umd.edu ▴ 30
0
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1
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1.3k
views
limmaGUI - venn-diagram & top-table anomaly?
limmaGUI limmaGUI
updated 15.3 years ago by ▴ 450 • written 15.3 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
16.1 years ago Christine Voellenkle ▴ 90
0
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1
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1.7k
views
statistics for differential expression: adjusted p-values<0.05 BUT negative B-odds?
Normalization limma limmaGUI Normalization limma limmaGUI
updated 16.2 years ago by ▴ 320 • written 16.2 years ago by ▴ 90
0
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1
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1.3k
views
asMatrixWeights: weights of unexpected shape
GUI limma limmaGUI GUI limma limmaGUI
updated 16.2 years ago by ▴ 90 • written 16.2 years ago by 52k
0
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3
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1.5k
views
duplicate correlation of 4 "within array replicates" limmaGUI
GUI limma limmaGUI microRNA GUI limma limmaGUI microRNA
16.2 years ago Gordon Smyth 52k
0
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2
replies
2.4k
views
problem with tkrplot installation
limmaGUI limmaGUI
updated 16.4 years ago by 67k • written 16.4 years ago by ▴ 20
0
votes
6
replies
2.5k
views
Is anyone developing an extensible Galaxy-like interface for Bioconductor?
affylmGUI limmaGUI affylmGUI limmaGUI
updated 16.4 years ago by ▴ 10 • written 16.4 years ago by ▴ 50
0
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2
replies
1.6k
views
Is anyone developing an extensible Galaxy-like interface for Bioconductor?
affylmGUI limmaGUI affylmGUI limmaGUI
updated 16.4 years ago by ▴ 90 • written 16.4 years ago by ▴ 140
0
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0
replies
1.1k
views
Is anyone developing an extensible Galaxy-like interface for Bioconductor?
Cancer affylmGUI limmaGUI Cancer affylmGUI limmaGUI
16.4 years ago Martin Morgan 25k
0
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2
replies
1.4k
views
limmaGUI: target file and spot file
limmaGUI limmaGUI
updated 16.4 years ago by ▴ 910 • written 16.4 years ago by ▴ 10
0
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0
replies
1.2k
views
error asMatrixWeights in LimmaGUI
Microarray limmaGUI Microarray limmaGUI
16.5 years ago bzzandrew@interfree.it ▴ 30
0
votes
1
reply
2.2k
views
Limma user’s guide example data sets
Microarray limma limmaGUI weaver Microarray limma limmaGUI weaver
updated 16.6 years ago by ▴ 130 • written 16.6 years ago by ▴ 450
0
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1
reply
1.4k
views
One-Color Agilent Data into Limma GUI
GO limma limmaGUI GO limma limmaGUI
updated 17.2 years ago by ★ 1.9k • written 17.2 years ago by ▴ 230
0
votes
2
replies
1.3k
views
help for limmaGUI
Microarray limmaGUI Microarray limmaGUI
updated 17.6 years ago by ★ 1.9k • written 17.6 years ago by ▴ 10
0
votes
3
replies
1.5k
views
limma: print-tip loess and empty spots
Normalization GO GUI limma limmaGUI Normalization GO GUI limma limmaGUI
17.6 years ago Gordon Smyth 52k
0
votes
0
replies
3.0k
views
Tcl/TK package "Bwidget" when using limmaGUI or affylmGUI
limmaGUI affylmGUI
updated 3 months ago by 52k • written 17.7 years ago by ▴ 450
0
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1
reply
1.3k
views
[Bioc] Tcl/TK pckage "Bwidget"
limmaGUI limmaGUI
updated 17.7 years ago by ▴ 10 • written 17.7 years ago by 21k
0
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0
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1.0k
views
Duplicated spots in limmaGUI
limmaGUI limmaGUI
17.7 years ago Gordon Smyth 52k
0
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1
reply
1.3k
views
Duplicated spots in limmaGUI
limmaGUI limmaGUI
updated 17.7 years ago by ▴ 500 • written 17.7 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 17.9 years ago by ★ 6.0k • written 17.9 years ago by ▴ 90
0
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0
replies
1.3k
views
Computing a diference of 2 differences from a CpG Island experiment using LimmaGUI
Cancer limmaGUI Cancer limmaGUI
18.2 years ago Darlene Goldstein ▴ 230
0
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0
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1.1k
views
limma citations [was LimmaGUI for illumina data]
Annotation GUI Kidney limma affylmGUI limmaGUI Annotation GUI Kidney limma affylmGUI
18.6 years ago Gordon Smyth 52k
0
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0
replies
1.2k
views
LimmaGUI for illumina data
GUI affy limma affylmGUI limmaGUI beadarray GUI affy limma affylmGUI limmaGUI beadarray
18.6 years ago Mark Dunning ▴ 320
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0
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1.0k
views
LimmaGUI for illumina data
GUI limma affylmGUI limmaGUI GUI limma affylmGUI limmaGUI
18.6 years ago Roy Williams ▴ 10
0
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1
reply
1.3k
views
reference design
limma limmaGUI oligo limma limmaGUI oligo
updated 18.6 years ago by ★ 6.0k • written 18.6 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
18.6 years ago bzzandrew@interfree.it ▴ 30
0
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3
replies
2.2k
views
Limma: correct calculation of B statistics (log odds)
limma limmaGUI limma limmaGUI
updated 18.7 years ago by ▴ 290 • written 18.7 years ago by ★ 1.9k
1
vote
3
replies
3.9k
views
Limma: correct calculation of B statistics (log odds)
Microarray Genetics limma limmaGUI Microarray Genetics limma limmaGUI
updated 18.7 years ago by ★ 1.9k • written 18.7 years ago by 52k
0
votes
1
reply
1.0k
views
Different results Limma vs LimmaGUI?
limma limmaGUI limma limmaGUI
updated 18.7 years ago by ★ 1.9k • written 18.7 years ago by 52k
0
votes
0
replies
995
views
Different results Limma vs LimmaGUI?
limma limmaGUI limma limmaGUI
18.7 years ago J.delasHeras@ed.ac.uk ★ 1.9k
0
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3
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2.5k
views
Limma: background correction. Use or ignore?
Microarray Cancer affy limma limmaGUI Microarray Cancer affy limma limmaGUI
updated 18.7 years ago by ★ 1.9k • written 18.7 years ago by 52k
50 results • Page 1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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