Showing : limma • reset
0
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6
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3.1k
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limma, analysis on subset of data gives completely different results
limma limma
updated 6 weeks ago by 50k • written 9.8 years ago by ▴ 40
1
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6
replies
2.7k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 7.5 years ago by ▴ 10
2
votes
8
replies
559
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
1
vote
3
replies
1.9k
views
Making MDS plot
plotMDS limma
updated 11 months ago by 50k • written 11 months ago by • 0
3
votes
11
replies
1.4k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 10 months ago by 50k • written 10 months ago by • 0
1
vote
6
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953
views
Limma dispersed distribution of log fold change
limma
written 8 months ago by • 0
5
votes
2
replies
597
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
0
votes
4
replies
392
views
limma with interaction term
R biostatistics limma Epigenetics
3 months ago • updated 11 weeks ago Jitendra ▴ 10
0
votes
2
replies
646
views
Fluidigm Data Batch Correction
sva limma
updated 10 months ago by 50k • written 10 months ago by • 0
8
votes
6
replies
501
views
DGE analysis with LIMMA
limma
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
1
vote
2
replies
473
views
Assess fit of variance prior
limma
updated 5 months ago by 50k • written 5 months ago by ▴ 20
9
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5
replies
5.1k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 5 months ago by 50k • written 8.2 years ago by ▴ 90
3
votes
2
replies
463
views
For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 10 months ago by 50k • written 10 months ago by • 0
1
vote
2
replies
395
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 13 days ago by 50k • written 13 days ago by • 0
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
26 days ago • updated 15 days ago Chris ▴ 10
1
vote
7
replies
873
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 5 months ago by 50k • written 7 months ago by • 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
votes
3
replies
479
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
11
votes
4
replies
1.9k
views
LIMMA dupcor() function time issue.
limma microarray block
updated 7 months ago by 50k • written 5.3 years ago by • 0
1
vote
3
replies
368
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 16 days ago by • 0 • written 13.1 years ago by ▴ 10
6
votes
5
replies
6.3k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 8 months ago by 50k • written 2.5 years ago by ▴ 340
2
votes
5
replies
1.4k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 9 months ago by 50k • written 9 months ago by • 0
0
votes
5
replies
964
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
7 months ago dorota.komar • 0
1
vote
3
replies
437
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
4
votes
2
replies
1.3k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 10 months ago by 50k • written 10 months ago by ▴ 10
0
votes
1
reply
152
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 14 days ago by 50k • written 14 days ago by • 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 23 days ago by • 0 • written 7.8 years ago by ▴ 30
0
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2
replies
315
views
limma model matrix questions
limmaGUI limma pairedsamples
12 weeks ago whyw6948 • 0
2
votes
4
replies
675
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 5 months ago by 50k • written 5 months ago by • 0
4
votes
7
replies
2.1k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by 50k • written 8.0 years ago by • 0
0
votes
1
reply
510
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
5
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3
replies
304
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 days ago by 50k • written 29 days ago by • 0
2
votes
1
reply
312
views
removeBatchEffect with non-linear model fit
limma DESeq2
updated 5 months ago by 50k • written 5 months ago by • 0
1
vote
1
reply
370
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 7 months ago by 65k • written 7 months ago by ▴ 10
1
vote
4
replies
744
views
Pairwise differential expression using limma
limma
10 months ago Melissa • 0
5
votes
6
replies
3.8k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 3 months ago by • 0 • written 3.2 years ago by ▴ 10
0
votes
2
replies
1.4k
views
Calculation of t-tests for factorial design
Microarray limma Microarray limma
written 13.7 years ago by ▴ 80
5
votes
25
replies
985
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 6 weeks ago by 50k • written 7 weeks ago by ▴ 10
5
votes
2
replies
700
views
PhD student
TMM limma
10 months ago Nisha • 0
5
votes
5
replies
823
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
9 months ago Jitendra ▴ 10
2
votes
4
replies
641
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
6 months ago Tyler Sagendorf ▴ 10
5
votes
9
replies
973
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 28 days ago Chris ▴ 10
0
votes
2
replies
292
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
3 months ago Lily Cheang ▴ 10
0
votes
6
replies
805
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 9 months ago by 50k • written 9 months ago by • 0
0
votes
3
replies
428
views
Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip limma goana
updated 5 months ago by ▴ 350 • written 5 months ago by • 0
0
votes
6
replies
865
views
Help with model.matrix and creating the right contrast matrix for limma
limma
8 months ago • updated 5 months ago rober204 • 0
0
votes
9
replies
588
views
limma fo continous variables
limma DEGseq
updated 11 weeks ago by 65k • written 12 weeks ago by • 0
2
votes
3
replies
386
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
1
vote
2
replies
614
views
Extracting fitted expression matrix from Limma
limma
11 months ago sarah.kelliher • 0
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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