Showing : Limma • reset
29
votes
0
replies
35k
views
limma moderated t-statistics and B-statistics
Microarray limma
19.0 years ago • updated 2.9 years ago Gordon Smyth 48k
31
votes
10
replies
34k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
updated 5 months ago by • 0 • written 9.8 years ago by ▴ 250
16
votes
14
replies
34k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 15 months ago by • 0 • written 6.2 years ago by ▴ 20
8
votes
10
replies
24k
views
Design formula and Design matrix in DESeq
rnaseq deseq2 formula Limma
8.4 years ago AurelieMLB ▴ 50
0
votes
7
replies
19k
views
DESeq2 batch correction best practice.
deseq2 limma RUVSeq
updated 3.2 years ago by 40k • written 3.2 years ago by • 0
6
votes
3
replies
17k
views
limma p-value and adjusted p-value meaning
limma
8.1 years ago arfranco ▴ 130
19
votes
11
replies
16k
views
when to apply quantile normalization with voom in limma/voom framework with RNA-seq data?
limma voom limma voom rna-seq quantile normalization
updated 7.6 years ago by 48k • written 7.7 years ago by ▴ 50
7
votes
6
replies
16k
views
Conversion of LogFC to FC
limma logfc fc
updated 3.5 years ago by 48k • written 3.5 years ago by ▴ 30
1
vote
1
reply
16k
views
Installation Problem: installation path not writeable, unable to update packages: MASS, mgcv, rpart
limma
updated 5.6 years ago by ▴ 300 • written 5.6 years ago by • 0
18
votes
37
replies
16k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma illumina differential gene expression multiple comparisons design matrix
8.3 years ago • updated 8.2 years ago svlachavas ▴ 810
2
votes
5
replies
15k
views
Limma design and contrast matrix question.
Microarray Regression limma Microarray Regression limma
updated 9.7 years ago by 63k • written 9.7 years ago by ▴ 350
0
votes
2
replies
15k
views
limma, FDR, and p.adjust
limma limma
updated 17 months ago by 48k • written 18.8 years ago by ▴ 890
21
votes
5
replies
13k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma voom
updated 8.4 years ago by 48k • written 9.3 years ago by ▴ 190
11
votes
5
replies
13k
views
Limma: how to get same output as topTable but for all the genes ?
limma toptable
updated 6.2 years ago by 48k • written 14.8 years ago by ▴ 190
3
votes
1
reply
12k
views
convert data in to expression set
limma convert limma convert
updated 10.3 years ago by ▴ 180 • written 10.3 years ago by ▴ 80
1
vote
12
replies
12k
views
Using limma for quantitative proteomics data
Microarray Proteomics limma Microarray Proteomics limma
11.3 years ago • updated 11.2 years ago Yong Li ▴ 80
9
votes
10
replies
12k
views
Is the following a correct usage of Limma's removeBatchEffect() for clustered heat map generation?
limma removeBatchEffect heatmap clustering
updated 7.7 years ago by ▴ 610 • written 7.7 years ago by ▴ 80
24
votes
12
replies
11k
views
Nanostring analysis with limma
nanostring limma
updated 8.4 years ago by ▴ 20 • written 8.4 years ago by ▴ 370
3
votes
1
reply
11k
views
How does limma t-test work?
Bayesian limma Bayesian limma
updated 11.1 years ago by 63k • written 11.1 years ago by ▴ 140
2
votes
6
replies
11k
views
DESeq2 vs limma/voom: PCA completely different. How to proceed?
limma DESeq2 limma DESeq2
updated 10.4 years ago by ★ 3.7k • written 10.4 years ago by ▴ 290
28
votes
8
replies
11k
views
Removing continuous covariate effects in limma analysis
limma microarray
updated 6.0 years ago by 48k • written 8.5 years ago by ▴ 150
13
votes
3
replies
11k
views
Understanding contrasts limma
limma design and contrast matrix
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 60
1
vote
5
replies
11k
views
Limma LogFC hand calculation
limma logfc
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
7
votes
4
replies
9.9k
views
Removing batch effect with limma::removeBatchEffect() actually exacerbates the effect
limma deseq2
updated 4.3 years ago by 48k • written 4.3 years ago by ▴ 20
10
votes
6
replies
9.7k
views
Estimating and removing batch effects from rna-seq dataset
sva batch effect rnaseq removebatcheffect() limma
updated 7.9 years ago by ▴ 640 • written 7.9 years ago by ▴ 110
0
votes
3
replies
9.4k
views
LIMMA: Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric
limma limma
updated 11.0 years ago by 63k • written 11.0 years ago by ▴ 180
22
votes
4
replies
9.1k
views
Correct assumptions of using limma moderated t-test
limma statistical inference variance test bioconductor
updated 8.3 years ago by 48k • written 8.3 years ago by ▴ 810
11
votes
8
replies
8.9k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 6.0 years ago by 48k • written 6.0 years ago by ▴ 80
3
votes
5
replies
8.9k
views
Problem Installing limma package
limma software error installation package installation
updated 6.4 years ago by 48k • written 6.4 years ago by • 0
2
votes
2
replies
8.9k
views
coefficient not estimable (limma warning)
limma limma
updated 12.4 years ago by ★ 6.0k • written 12.4 years ago by ▴ 440
5
votes
5
replies
8.6k
views
How to make contrast table to combine two conditions/treatments against another one (in a multi groups experiments
limma design and contrast matrix
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 20
14
votes
12
replies
8.3k
views
limma lmFit coefficients and p-values
limma methylation ewas
updated 7.1 years ago by 13k • written 7.1 years ago by ▴ 30
1
vote
8
replies
8.0k
views
"Subscript out of bounds" erorr during microarray analysis with Limma
oligo limma bioconductor affymetrix microarrays
8.2 years ago Claudia ▴ 10
1
vote
3
replies
8.0k
views
Annotating limma Results with Gene Names for Affy Microarrays
limma annotation pd.mogene.2.0.st mogene20sttranscriptcluster.db affy
updated 8.7 years ago by 48k • written 8.8 years ago by ▴ 130
0
votes
5
replies
8.0k
views
Limma topTable; fold changes look completely different to the normalized data and Limma fold change
limma limma
11.2 years ago john herbert ▴ 560
21
votes
7
replies
8.0k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma deseq2 edger rnaseq
updated 6.0 years ago by 48k • written 6.0 years ago by • 0
2
votes
4
replies
7.7k
views
Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimension
limma differential expression design matrix error eset
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 20
8
votes
15
replies
7.7k
views
Design matrix for continuous independent variable in limma
limma microarray
7.7 years ago Linda Chaba ▴ 10
4
votes
7
replies
7.7k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 20
6
votes
7
replies
7.6k
views
batch effect : comBat or blocking in limma ?
batch effect combat limma block
updated 8.0 years ago by 7.8k • written 8.0 years ago by ▴ 60
3
votes
5
replies
7.5k
views
limma voom accessing normalised counts tables
limma rnaseq geneexpression voom counts
updated 8.9 years ago by 13k • written 8.9 years ago by ▴ 10
7
votes
8
replies
7.5k
views
removeBatchEffect options: design and covariates
limma removebatcheffect
updated 6.0 years ago by 48k • written 9.1 years ago by ▴ 550
7
votes
18
replies
7.5k
views
Differential expression analysis: Continuous variables
DESeq EdgeR limma
8.0 years ago Radek ▴ 90
10
votes
3
replies
7.5k
views
Volcanoplot with limma - RAW P-values or Adj.P-Values
volcanoplot limma fdr
6.2 years ago • updated 2.8 years ago tcalvo ▴ 90
3
votes
2
replies
7.4k
views
Limma paired sample analysis
limma design matrix limma paired analysis limma
6.0 years ago anandprem1792 ▴ 20
2
votes
4
replies
7.4k
views
Limma design and contrast matrix
limma limma design matrix limma contrast matrix
7.5 years ago donny.dw • 0
12
votes
9
replies
7.3k
views
Appropriate use of the function treat of the limma package
limma treat microarray bioconductor
8.5 years ago svlachavas ▴ 810
3
votes
3
replies
7.3k
views
TPM data Differential expression analysis
edger limma differential gene expression
updated 16 months ago by 48k • written 5.4 years ago by • 0
3
votes
4
replies
7.3k
views
edgeR design matrix and contrasts: how to make contrast between groups that aren't shown in the design matrix columns?
edger design and contrast matrix contrast limma contrast matrix limma
updated 5.7 years ago by 48k • written 5.7 years ago by ▴ 20
3
votes
3
replies
7.2k
views
Gene Set Enrichment Analysis with Limma
limma romer gene set analysis
updated 7.8 years ago by 48k • written 7.8 years ago by ▴ 40
50 results • Page 1 of 1
Recent ...
Replies
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?
Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k
> So do you means the specification change from DelayedArray's read_sparse_block to SparseArray's read_block_as_sparse will accelerate the …
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Thanks for your reply. So do you means the specification change from `DelayedArray`'s `read_sparse_block` to `SparseArray`'s `read_block_a…
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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