Showing : limma • reset
1
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2
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325
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 2 days ago by 50k • written 2 days ago by • 0
0
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1
reply
97
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 3 days ago by 50k • written 3 days ago by • 0
3
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4
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205
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Help with error using camera() in limma
CAMERA limma
5 days ago Chris • 0
0
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3
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239
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 5 days ago by 65k • written 6 days ago by • 0
0
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2
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165
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 13 days ago by • 0
0
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2
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212
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
16 days ago • updated 14 days ago catv • 0
14
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17
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1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
16 days ago • updated 4 days ago Chris • 0
3
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1
reply
177
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Log-cpm values from limma
limma edgeR RNASeq
updated 17 days ago by 50k • written 18 days ago by • 0
0
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7
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319
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
19 days ago • updated 13 days ago hortense96 • 0
1
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3
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351
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 21 days ago by 50k • written 26 days ago by • 0
5
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9
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929
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Light difference when using coef vs omit a group when compare 3 groups.
limma
25 days ago • updated 18 days ago Chris • 0
2
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6
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401
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
27 days ago Chris • 0
0
votes
1
reply
168
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
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4
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313
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Help with design.matrix
limma
4 weeks ago • updated 29 days ago andrea.rodriguez-martinez13 • 0
1
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4
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442
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
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2
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191
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
4 weeks ago Gimena • 0
15
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23
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2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 5 days ago Chris • 0
2
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8
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539
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
5
votes
25
replies
937
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 4 weeks ago by 50k • written 5 weeks ago by ▴ 10
7
votes
6
replies
458
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
1
reply
235
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
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4
replies
395
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
7 weeks ago • updated 5 weeks ago Efra • 0
5
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7
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457
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 5 weeks ago by 50k • written 7 weeks ago by • 0
2
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2
replies
263
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
0
votes
2
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269
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
7 weeks ago kcarey • 0
1
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3
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409
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
2
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6
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488
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
8 weeks ago • updated 5 weeks ago Lily Cheang ▴ 10
3
votes
8
replies
515
views
Constrast for Time Course Experiments using Limma
limma
8 weeks ago dl17032000 • 0
8
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6
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459
views
DGE analysis with LIMMA
limma
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
0
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0
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151
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Can I combine collinear variables into a single value
BatchEffect limma
9 weeks ago Harrsha • 0
0
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3
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287
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
0
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4
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303
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 weeks ago mperalc • 0
3
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5
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631
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 weeks ago by 41k • written 10 weeks ago by ▴ 10
2
votes
1
reply
266
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 10 weeks ago by 41k • written 10 weeks ago by ▴ 10
1
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2
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310
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Bioconductor unreachable?
limma
10 weeks ago edoardo • 0
0
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9
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563
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limma fo continous variables
limma DEGseq
updated 9 weeks ago by 65k • written 10 weeks ago by • 0
0
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2
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296
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limma model matrix questions
limmaGUI limma pairedsamples
10 weeks ago whyw6948 • 0
0
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2
replies
321
views
Limma with replicates at different time points
RNAs limma Differen
11 weeks ago • updated 9 weeks ago alessandro • 0
2
votes
1
reply
302
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 11 weeks ago by ★ 4.1k • written 11 weeks ago by • 0
1
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3
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357
views
CAMERA + Gene Ontology Gene Sets
GO limma CAMERA
updated 12 weeks ago by 50k • written 12 weeks ago by ▴ 10
0
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4
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372
views
limma with interaction term
R biostatistics limma Epigenetics
12 weeks ago • updated 10 weeks ago Jitendra ▴ 10
3
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2
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297
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
12 weeks ago Shaimaa Gamal • 0
2
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3
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328
views
Longitudinal analysis in Limma: Block=ID as random effect
limma
12 weeks ago COPD_Project • 0
2
votes
2
replies
291
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
3 months ago • updated 12 weeks ago SamGG ▴ 350
1
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4
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412
views
limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 12 weeks ago by 50k • written 12 weeks ago by ▴ 10
4
votes
3
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357
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
2
votes
3
replies
371
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months 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 12 months ago by • 0
0
votes
2
replies
263
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
3 months ago Lily Cheang ▴ 10
1
vote
2
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346
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Longitudinal analysis in Limma
limma
3 months ago COPD_Project • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Trim/Filter out-of-bounds GRanges by Michael Love 41k
https://support.bioconductor.org/p/73432/#73448
Comment: Couldn't connect to server while using "pathways" by Michael Love 41k
You've put the tag "DESeq2" which results in an email to the maintainer, me, that I should respond to a post on the support site. Can you …
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Vincent J. Carey, Jr. 6.7k
btw that was run on M1 mac
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Vincent J. Carey, Jr. 6.7k
the test is not portable > aa <- aa_mutmat(acc = "MIYS930101", aaindex = "aaindex2") > str(aa) num [1:20, 1:20] 0.34 -0.0…
Comment: Method to find pathways different between 2 groups by Chris • 0
Sorry for not clear! Glad to know camera() is widely used. I just try to find papers use this method for learning purpose. Which gives more…
Votes
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
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