Showing : Limma • reset
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 2 days ago by 50k • written 2 days ago by • 0
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2
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149
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
5 days ago • updated 2 days ago catv • 0
12
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12
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754
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Why p value inconsistent when using different number of pathway score?
limma
updated 3 days ago by ★ 3.3k • written 4 days ago by • 0
3
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1
reply
112
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Log-cpm values from limma
limma edgeR RNASeq
updated 5 days ago by 50k • written 6 days ago by • 0
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7
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239
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
7 days ago • updated 1 day ago hortense96 • 0
1
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3
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320
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 9 days ago by 50k • written 15 days ago by • 0
5
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9
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853
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Light difference when using coef vs omit a group when compare 3 groups.
limma
14 days ago • updated 6 days ago Chris • 0
2
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6
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342
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
16 days ago Chris • 0
0
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1
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144
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Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 18 days ago by 50k • written 19 days ago by • 0
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4
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289
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Help with design.matrix
limma
19 days ago • updated 18 days ago andrea.rodriguez-martinez13 • 0
1
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4
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412
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 20 days ago by 50k • written 21 days ago by • 0
0
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2
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169
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
21 days ago Gimena • 0
15
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22
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1.8k
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The difference when using Limma compare between 3 conditions vs 2 conditions
limma
26 days ago • updated 4 days ago Chris • 0
2
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8
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486
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 28 days ago by 50k • written 29 days ago by • 0
5
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25
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818
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limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 20 days ago by 50k • written 4 weeks ago by ▴ 10
7
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6
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429
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Batch Effect Correction, Gene Filtering
DGE limma
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
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1
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214
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
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4
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367
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
5 weeks ago • updated 4 weeks ago Efra • 0
5
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7
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427
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DEG Filtering
MicroarrayData limma Genefiltering
updated 28 days ago by 50k • written 5 weeks ago by • 0
2
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2
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244
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 weeks ago • updated 5 weeks ago Sabiha ▴ 20
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2
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236
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago • updated 5 weeks ago kcarey • 0
0
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3
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359
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
2
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6
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443
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limma: vooma mean-variance trend and data filtration
MicroarrayData limma
7 weeks ago • updated 4 weeks ago Lily Cheang ▴ 10
3
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8
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480
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Constrast for Time Course Experiments using Limma
limma
7 weeks ago • updated 6 weeks ago dl17032000 • 0
8
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6
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425
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DGE analysis with LIMMA
limma
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
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0
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141
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Can I combine collinear variables into a single value
BatchEffect limma
7 weeks ago Harrsha • 0
0
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3
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268
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Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
0
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4
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273
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
8 weeks ago • updated 7 weeks ago mperalc • 0
3
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5
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600
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 weeks ago by 41k • written 8 weeks ago by ▴ 10
2
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1
reply
243
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 weeks ago by 41k • written 8 weeks ago by ▴ 10
1
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2
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277
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Bioconductor unreachable?
limma
8 weeks ago edoardo • 0
0
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9
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530
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limma fo continous variables
limma DEGseq
updated 8 weeks ago by 65k • written 9 weeks ago by • 0
0
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2
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271
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limma model matrix questions
limmaGUI limma pairedsamples
9 weeks ago whyw6948 • 0
0
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2
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301
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Limma with replicates at different time points
RNAs limma Differen
9 weeks ago • updated 8 weeks ago alessandro • 0
2
votes
1
reply
280
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 9 weeks ago by ★ 4.0k • written 10 weeks ago by • 0
1
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3
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332
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CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 10
0
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4
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340
views
limma with interaction term
R biostatistics limma Epigenetics
10 weeks ago • updated 8 weeks ago Jitendra ▴ 10
3
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2
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272
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
11 weeks ago • updated 10 weeks ago Shaimaa Gamal • 0
2
votes
3
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305
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
11 weeks ago • updated 10 weeks ago COPD_Project • 0
2
votes
2
replies
268
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
11 weeks ago SamGG ▴ 350
1
vote
4
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378
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limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 10 weeks ago by 50k • written 11 weeks ago by ▴ 10
4
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3
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333
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
2
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3
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351
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
1
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2
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1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
0
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2
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242
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Pairwise analysis of DESeq result and limma result
DESeq2 limma
11 weeks ago Lily Cheang ▴ 10
1
vote
2
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317
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Longitudinal analysis in Limma
limma
12 weeks ago COPD_Project • 0
2
votes
2
replies
265
views
Using limma for controlling age variable
linearmodeling limma
12 weeks ago Matej • 0
4
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6
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555
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 weeks ago by 50k • written 3 months ago by • 0
0
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5
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515
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
2
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4
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489
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 3 months ago by 50k • written 4 months ago by • 0
50 results • Page 1 of 1
Recent ...
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Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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