Showing : Limma • reset
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''Model_Matrix'' error
DifferentialExpression limma
updated 21 minutes ago by 48k • written 13 hours ago by • 0
1
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6
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2.1k
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Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 6.9 years ago by ▴ 10
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46
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Huge effect of a single sample on DEGs
limma
1 day ago Jonathan • 0
0
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1
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41
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Further analysis after limma regression output
statistics Epigenetics limma
updated 1 day ago by 63k • written 1 day ago by ▴ 10
3
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3
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153
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comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 3 days ago by 63k • written 4 days ago by • 0
3
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3
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384
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Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
4 days ago • updated 3 days ago Ethan Nguyen • 0
1
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2
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125
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Should I use CPM or Voom transformed values for downstream analysis?
edgeR limma
5 days ago • updated 4 days ago petertam1343 • 0
0
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3
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230
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Help with model.matrix and creating the right contrast matrix for limma
limma
updated 8 days ago by 48k • written 10 days ago by • 0
5
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5
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3.9k
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Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 11 days ago by 48k • written 22 months ago by ▴ 330
3
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4
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339
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Phenotype effect - building a contrast matrix - grouping vs interaction
limma
12 days ago • updated 11 days ago Jonathan • 0
3
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10
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532
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Timely differentially expressed genes
timecoursedata limma
updated 3 days ago by 48k • written 17 days ago by • 0
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188
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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 23 days ago by ★ 3.4k • written 23 days ago by • 0
1
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6
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284
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Limma dispersed distribution of log fold change
limma
written 25 days ago by • 0
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0
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113
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Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
25 days ago svlachavas ▴ 810
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2
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182
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How to incorporate covariate factors into design to analyse a continuous variable?
DifferentialMethylation limma
written 5 weeks ago by • 0
1
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3
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238
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Can CAMERA analyze just one particular pathway
pathway ORA limma CAMERA DGE
updated 4 weeks ago by 48k • written 5 weeks ago by • 0
5
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5
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297
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limma output for epic array methylation data
linearregression epicarray MethylationArray limma
5 weeks ago Jitendra ▴ 10
2
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5
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348
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removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 6 weeks ago by 48k • written 6 weeks ago by • 0
1
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3
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233
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bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 6 weeks ago by 63k • written 6 weeks ago by • 0
5
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7
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306
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Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 7 weeks ago by 48k • written 7 weeks ago by • 0
1
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2
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266
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loading scores using plotMDS in limma
plotMDS limma
8 weeks ago • updated 6 weeks ago Cen • 0
2
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1
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246
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Grouping DEGs yields varying results
RNASeq limma
updated 8 weeks ago by 48k • written 8 weeks ago by • 0
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6
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370
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 8 weeks ago by 48k • written 8 weeks ago by • 0
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2
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262
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Fluidigm Data Batch Correction
sva limma
updated 9 weeks ago by 48k • written 10 weeks ago by • 0
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2
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237
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smallRNA-seq analysis batch correction in limma
BatchEffect limma
9 weeks ago Eleonora • 0
3
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2
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229
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For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 9 weeks ago by 48k • written 9 weeks ago by • 0
1
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1
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302
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 10 weeks ago by 48k • written 10 weeks ago by • 0
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4
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293
views
Pairwise comparison for DEG analysis
limma
updated 9 weeks ago by ★ 3.4k • written 10 weeks ago by • 0
3
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2
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375
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 11 weeks ago by 48k • written 11 weeks ago by • 0
1
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1
reply
232
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 11 weeks ago by 48k • written 11 weeks ago by • 0
3
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2
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350
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PhD student
TMM limma
11 weeks ago Nisha • 0
1
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5
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504
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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 11 weeks ago by 48k • written 12 weeks ago by • 0
1
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4
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408
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Pairwise differential expression using limma
limma
12 weeks ago • updated 11 weeks ago Melissa • 0
2
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3
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359
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how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq RNASeqData sva limma
12 weeks ago amnahsiddiqa • 0
0
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2
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233
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Visualization of absolute values after batch effect correction
limma
updated 12 weeks ago by ▴ 300 • written 12 weeks ago by • 0
0
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1
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202
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How to do PFS after Voom + Limma DGE ?
RNASeqData limma voom PFS DGE
updated 12 weeks ago by 63k • written 12 weeks ago by • 0
3
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11
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799
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SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 3 months ago by 48k • written 3 months ago by • 0
0
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2
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308
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decideTests vs topTable results
decideTests topTable limma
updated 3 months ago by 48k • written 3 months ago by ▴ 20
0
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3
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320
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limma paired design
DifferentialExpression limma
updated 3 months ago by 63k • written 3 months ago by • 0
0
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2
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336
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RNA seq differential expression analysis
DEGseq RNASeqData limma
updated 3 months ago by 48k • written 3 months ago by • 0
1
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3
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476
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Making MDS plot
plotMDS limma
updated 3 months ago by 48k • written 3 months ago by • 0
0
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3
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339
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Extract Limma Adjusted Values for Plotting
limma
updated 3 months ago by ★ 3.4k • written 3 months ago by • 0
3
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6
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477
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 3 months ago by 48k • written 3 months ago by ▴ 10
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2
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328
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Extracting fitted expression matrix from Limma
limma
3 months ago sarah.kelliher • 0
3
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11
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976
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
4 months ago • updated 3 months ago Anna ▴ 20
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2
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322
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Nanostring data differential expression analysis: limma or DESeq2?
DESeq2 NanoStringDiff limma
4 months ago pg45863 • 0
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5
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472
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Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
4 months ago pg45863 • 0
0
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1
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271
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DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 4 months ago by ★ 1.3k • written 4 months ago by • 0
0
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1
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277
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LIMMA: design with paired samples within and across treatments
DifferentialExpression limma
updated 4 months ago by 48k • written 4 months ago by • 0
3
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4
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406
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Anova table edgeR limma
limma RNASeq edgeR
4 months ago KATHERINE CHUERE NUNES • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: ''Model_Matrix'' error by Gordon Smyth 48k
This is actually an error message from base R rather than from limma. The error says that `Group` contains only one value, so your assumpti…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
> I don't know the details but do you mean using HDF5RealizationSink or TENxRealizationSink will make it possible to writing sparse multi-d…
Comment: DMRcate design by Jitendra ▴ 10
Thanks James, do I also need to mention 'contrasts=FALSE' in cpg.annotate.And also what to mentions in analysis.type="differential",/ "ANO…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
I don't know the details but do you mean using `HDF5RealizationSink` or `TENxRealizationSink` will make it possible to writing sparse multi…
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Ok, I understood. How about "writing" to HDF5? Are you going to implement `write_block_as_sparse` in `SparseArray` package?
Votes
Steps needed to change design (relevel factors) in DESeq2
Steps needed to change design (relevel factors) in DESeq2
Answer: DMRcate design
Answer: DMRcate design
Comment: DMRcate design
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