Showing : limma • reset
1
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6
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2.7k
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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 7.5 years ago by ▴ 10
0
votes
6
replies
3.1k
views
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
2
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8
replies
568
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
1
vote
6
replies
954
views
Limma dispersed distribution of log fold change
limma
written 8 months ago by • 0
9
votes
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
15
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17
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1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
4 weeks ago • updated 18 days ago Chris ▴ 10
8
votes
6
replies
509
views
DGE analysis with LIMMA
limma
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
0
votes
4
replies
396
views
limma with interaction term
R biostatistics limma Epigenetics
3 months ago • updated 12 weeks ago Jitendra ▴ 10
1
vote
2
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81
views
Subsetting RNAseq data | voomaByGroup()
limma
2 days ago • updated 1 hour ago Anna • 0
6
votes
5
replies
6.4k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 8 months ago by 50k • written 2.5 years ago by ▴ 340
3
votes
11
replies
1.4k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 11 months ago by 50k • written 11 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
3
votes
2
replies
465
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
407
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 16 days ago by 50k • written 16 days ago by • 0
1
vote
2
replies
475
views
Assess fit of variance prior
limma
updated 5 months ago by 50k • written 5 months ago by ▴ 20
1
vote
3
replies
1.9k
views
Making MDS plot
plotMDS limma
updated 11 months ago by 50k • written 11 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
484
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
6 months ago • updated 5 months ago Karthik • 0
0
votes
2
replies
651
views
Fluidigm Data Batch Correction
sva limma
updated 10 months ago by 50k • written 10 months ago by • 0
1
vote
3
replies
369
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 5 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 19 days ago by • 0 • written 13.1 years ago by ▴ 10
1
vote
7
replies
884
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
0
votes
5
replies
975
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
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
443
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
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
5
votes
2
replies
607
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
1
reply
163
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 17 days ago by 50k • written 17 days 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
2
replies
322
views
limma model matrix questions
limmaGUI limma pairedsamples
3 months ago whyw6948 • 0
5
votes
3
replies
317
views
Log-cpm values from limma
limma edgeR RNASeq
updated 10 days ago by 50k • written 4 weeks ago by • 0
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 27 days ago by • 0 • written 7.8 years ago by ▴ 30
1
vote
3
replies
667
views
Can CAMERA analyze just one particular pathway
pathway ORA limma CAMERA DGE
updated 9 months ago by 50k • written 9 months ago by • 0
2
votes
1
reply
314
views
removeBatchEffect with non-linear model fit
limma DESeq2
updated 5 months ago by 50k • written 5 months ago by • 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
9
replies
593
views
limma fo continous variables
limma DEGseq
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
0
votes
3
replies
431
views
Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip limma goana
updated 5 months ago by ▴ 350 • written 5 months ago by • 0
1
vote
1
reply
374
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 8 months ago by 65k • written 8 months 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
0
votes
1
reply
515
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
votes
5
replies
827
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
9 months ago Jitendra ▴ 10
2
votes
4
replies
646
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
6 months ago Tyler Sagendorf ▴ 10
0
votes
2
replies
304
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
3 months ago Lily Cheang ▴ 10
5
votes
9
replies
980
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 4 weeks ago Chris ▴ 10
0
votes
6
replies
812
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 10 months ago by 50k • written 10 months ago by • 0
5
votes
2
replies
703
views
PhD student
TMM limma
10 months ago Nisha • 0
1
vote
2
replies
615
views
Extracting fitted expression matrix from Limma
limma
11 months ago sarah.kelliher • 0
1
vote
4
replies
748
views
Pairwise differential expression using limma
limma
10 months ago Melissa • 0
0
votes
6
replies
872
views
Help with model.matrix and creating the right contrast matrix for limma
limma
8 months ago • updated 5 months ago rober204 • 0
1
vote
12
replies
2.5k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma highthroughputassays R
updated 3 months ago by • 0 • written 2.6 years ago by ▴ 380
50 results • Page 1 of 1
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Answer: ERROR; return code from pthread_create() is 22 by James W. MacDonald 65k
Seems OK to me. ``` > dat <- ReadAffy() > dat AffyBatch object size of arrays=744x744 features (20 kb) cdf=HG-U219 (49386 affyids) …
Answer: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 65k
Unless you think the different lines or tissues will have very different within-group variances, you should just analyze together and make …
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments? by James W. MacDonald 65k
It appears that batch is orthogonal to the treatment, so you can just fit a batch effect in your model.
Answer: Control group between 2 batches have different expression in RNAseq data by James W. MacDonald 65k
Since batch is orthogonal to the treatment, you just add a batch factor to your model.
Answer: Subsetting RNAseq data | voomaByGroup() by Anna • 0
Hi Gordon. Thank you so much. Your reply is extremely helpful, and I feel more confident moving forward with the analysis. Also, very inte…
Votes
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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