Showing : limma • reset
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3
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142
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Extract Limma Adjusted Values for Plotting
limma
updated 2 days ago by ★ 2.9k • written 3 days ago by • 0
3
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6
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264
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 5 days ago by 47k • written 6 days ago by ▴ 10
1
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2
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158
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Extracting fitted expression matrix from Limma
limma
10 days ago • updated 8 days ago sarah.kelliher • 0
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11
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457
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Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
10 days ago • updated 1 day ago Anna ▴ 20
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2
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98
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Nanostring data differential expression analysis: limma or DESeq2?
DESeq2 NanoStringDiff limma
12 days ago pg45863 • 0
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5
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236
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Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
13 days ago • updated 12 days ago pg45863 • 0
0
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1
reply
132
views
DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 12 days ago by ★ 1.2k • written 13 days ago by • 0
0
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1
reply
144
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LIMMA: design with paired samples within and across treatments
DifferentialExpression limma
updated 24 days ago by 47k • written 24 days ago by • 0
3
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4
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228
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Anova table edgeR limma
limma RNASeq edgeR
25 days ago • updated 24 days ago KATHERINE CHUERE NUNES • 0
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2
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169
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 4 weeks ago by • 0
1
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2
replies
137
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Contrast of Contrasts in Limma
limma DifferentialExpression
28 days ago • updated 27 days ago mpitz • 0
1
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3
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220
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Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 4 weeks ago by 47k • written 4 weeks ago by • 0
0
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0
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115
views
Volcano plot
limma AffymetrixChip
4 weeks ago e.gunaut • 0
0
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2
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194
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Limma multi-group, nested analysis with aggregation
limma
5 weeks ago • updated 4 weeks ago Jonathan • 0
0
votes
1
reply
160
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 5 weeks ago by 47k • written 5 weeks ago by • 0
2
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3
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262
views
Using gcrma() and using the t-test to compare single genes of interest for disease vs healthy comparison?
gcrma CustomCDF Affyhgu133aExpr limma affy
updated 7 weeks ago by 63k • written 7 weeks ago by ▴ 10
1
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2
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204
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
7 weeks ago Abdul ▴ 20
2
votes
2
replies
267
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
8 weeks ago Abdul ▴ 20
0
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2
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218
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RPPA data (Proteomics analysis)
TCGAbiolinks limma
9 weeks ago • updated 5 weeks ago qiz218591 • 0
0
votes
2
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164
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 9 weeks ago by 47k • written 9 weeks ago by • 0
1
vote
4
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816
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
2.7 years ago • updated 9 weeks ago linouhao ▴ 20
2
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4
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269
views
limma with or without intercept gives different results
limma rnaseq
10 weeks ago • updated 9 weeks ago Sydney • 0
0
votes
1
reply
149
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Handling limma usage after running multiple imputation on the covariates with missing data
limma
updated 10 weeks ago by 47k • written 10 weeks ago by • 0
0
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3
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296
views
[limma::kegga] Pathway names all NA
KEGG limma
updated 10 weeks ago by 47k • written 10 weeks ago by • 0
0
votes
1
reply
150
views
Limma for Fluidigm high throughput PCR
limma Limma Fluidigm
updated 10 weeks ago by 47k • written 11 weeks ago by • 0
1
vote
4
replies
255
views
How to deal with the negative values from EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2 when DEGs
limma edgeR RSEM
updated 10 weeks ago by 47k • written 11 weeks ago by ▴ 10
2
votes
7
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402
views
limma: contrasting two groups of which one is completely missing returns small p-value
limma
updated 11 weeks ago by 47k • written 11 weeks ago by ▴ 30
0
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0
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101
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Limma: Models containing an intercept and interactions with continuous variables.
limma edgeR DifferentialExpression
11 weeks ago Aashil • 0
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0
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201
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Some questions regarding using limma and interpretation
limma
11 weeks ago Sep • 0
1
vote
2
replies
169
views
Differential expression analysis based on EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2
DESeq2 limma edgeR RSEM
12 weeks ago • updated 11 weeks ago Yang Shi ▴ 10
0
votes
1
reply
153
views
specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 12 weeks ago by 63k • written 12 weeks ago by • 0
2
votes
2
replies
197
views
Question about avereps function of limma
avereps probes average limma Microarray
updated 12 weeks ago by 47k • written 12 weeks ago by ▴ 10
0
votes
2
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220
views
Is there any reason to think that normalization (e.g. TMM) doesn't work well with samples that that have very different raw counts?
limma RNASeqData edgeR
updated 3 months ago by ▴ 30 • written 3 months ago by • 0
0
votes
1
reply
202
views
Microarray Data - Matching Probe ID's to Gene Expression Symbols
limma
updated 3 months ago by 3.8k • written 3 months ago by • 0
1
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3
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245
views
Calculating the contrast of two genotypes "vs"
limma
updated 3 months ago by 47k • written 3 months ago by ▴ 10
0
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17
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635
views
How to check linear model
modalmatrix limma R linear
3 months ago Jitendra ▴ 10
6
votes
11
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569
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
3 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
249
views
Differential expression analysis with global differences among samples (tissues)
DESeq2 qsmooth edgeR limma
updated 3 months ago by 47k • written 3 months ago by • 0
5
votes
2
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289
views
Sva and batch effect
limma BatchEffect sva
updated 4 months ago by 47k • written 4 months ago by • 0
1
vote
3
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244
views
Limma-voom with inverse probability weights (similar to sample weights)
limma limma-voom StatisticalMethod
updated 4 months ago by 47k • written 4 months ago by • 0
2
votes
4
replies
275
views
Reproducibility using limma for DE Analysis
limma seed DifferentialRegulation
updated 4 months ago by 47k • written 4 months ago by • 0
4
votes
1
reply
397
views
on which data type limma::removeBatchEffect can be applyed?
batch limma
updated 4 months ago by ★ 2.9k • written 4 months ago by ▴ 40
3
votes
5
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427
views
Design for DE analysis in tidybulk
DESeq2 designmatrix edgeR limma tidybulk
updated 4 months ago by 40k • written 4 months ago by ▴ 10
0
votes
1
reply
989
views
limma: decideTests
affy limma affy limma
updated 4 months ago by 47k • written 15.5 years ago by ▴ 270
0
votes
1
reply
168
views
NAs in some genes in topTable output
limma topTable
updated 4 months ago by 47k • written 4 months ago by ▴ 10
0
votes
1
reply
173
views
limma on spectral data
limma Metabolomics DifferentialExpression POMA
updated 4 months ago by 47k • written 4 months ago by • 0
0
votes
2
replies
393
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 4 months ago by 47k • written 4 months ago by • 0
3
votes
4
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373
views
Processing data with voom "expression values" and "weights"
limma voom
updated 4 months ago by 47k • written 4 months ago by • 0
2
votes
2
replies
257
views
Estimating Fold-Changes of Lowly Expressed Genes
limma
4 months ago vm ▴ 30
0
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2
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284
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
4 months ago dqt • 0
50 results • Page 1 of 1
Recent ...
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Comment: Ensembl plants at annotationHub? by Bruno • 0
Hi Guido, Thanks for your fast reply the error was as said in my question "Annotation must be a GRanges object", when I tried to use the a…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 3.6k
You did not show the code that resulted in that error, so we have to guess what you did. Yet, the [R package][1] `Signac` contains the func…
Comment: Query regarding phyloseq object construct with QIIME output by betterwound • 0
Thanks for sharing the code [geometry dash](https://geometrydash.io/)
Answer: Ensembl plants at annotationHub? by Bruno • 0
Hi Johannes, First, thank you so much for providing these annotations for the community. We feel often a bit left off in the plant commu…
Comment: DESeq2 on multilevel design variable by swbarnes2 ★ 1.2k
Did you relevel before or after calling DESeq?
Votes
Comment: DESeq2 on multilevel design variable
Comment: Ensembl plants at annotationHub?
Answer: DESeq2 on multilevel design variable
Comment: Sudden error with KEGG analysis using gometh
Comment: Sudden error with KEGG analysis using gometh
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