Showing : limma • reset
1
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6
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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 29 days ago by 50k • written 9.8 years ago by ▴ 40
2
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8
replies
515
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
9
votes
5
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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
6
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5
replies
6.2k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 7 months ago by 50k • written 2.5 years ago by ▴ 340
3
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2
replies
444
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For limma, if I leave coef=NULL, which test is the P value for?
limma
updated 9 months ago by 50k • written 9 months ago by • 0
0
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3
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1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 1 day ago by • 0 • written 13.0 years ago by ▴ 10
0
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4
replies
361
views
limma with interaction term
R biostatistics limma Epigenetics
11 weeks ago • updated 9 weeks ago Jitendra ▴ 10
1
vote
3
replies
340
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 16 days ago by 50k • written 22 days ago by • 0
5
votes
2
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547
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Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 4 months ago by • 0
3
votes
11
replies
1.3k
views
SD filtering before DEG analysis with limma : possible or not ?
filtering STD DEG limma
updated 10 months ago by 50k • written 10 months ago by • 0
1
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3
replies
1.8k
views
Making MDS plot
plotMDS limma
updated 10 months ago by 50k • written 10 months ago by • 0
0
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7
replies
1.4k
views
A question about Limma
PROcess Microarray limma
19.3 years ago • updated 11 months ago Gordon Smyth 50k
1
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6
replies
916
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Limma dispersed distribution of log fold change
limma
written 8 months ago by • 0
1
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2
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460
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Assess fit of variance prior
limma
updated 4 months ago by 50k • written 4 months ago by ▴ 20
14
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17
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1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
11 days ago • updated 12 hours ago Chris • 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
3
replies
452
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
0
votes
2
replies
615
views
Fluidigm Data Batch Correction
sva limma
updated 9 months ago by 50k • written 9 months ago by • 0
8
votes
6
replies
445
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DGE analysis with LIMMA
limma
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
1
vote
3
replies
394
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
1
vote
7
replies
828
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 4 months ago by 50k • written 6 months ago by • 0
2
votes
5
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1.3k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 8 months ago by 50k • written 8 months ago by • 0
0
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5
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911
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
6 months ago dorota.komar • 0
4
votes
2
replies
1.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 9 months ago by 50k • written 10 months ago by ▴ 10
11
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4
replies
1.8k
views
LIMMA dupcor() function time issue.
limma microarray block
updated 7 months ago by 50k • written 5.2 years ago by • 0
3
votes
5
replies
882
views
limma-trend vs. limma-voom theoretical difference
limma limma-trend limma-voom
updated 3 months ago by ▴ 30 • written 17 months ago by • 0
7
votes
6
replies
443
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
2
votes
4
replies
626
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 4 months ago by 50k • written 4 months ago by • 0
0
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2
replies
312
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Limma with replicates at different time points
RNAs limma Differen
10 weeks ago • updated 9 weeks ago alessandro • 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 8 days ago by • 0 • written 7.7 years ago by ▴ 30
5
votes
6
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3.8k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 3 months ago by • 0 • written 3.1 years ago by ▴ 10
0
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2
replies
283
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limma model matrix questions
limmaGUI limma pairedsamples
10 weeks ago whyw6948 • 0
4
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7
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2.1k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by 50k • written 7.9 years ago by • 0
3
votes
1
reply
156
views
Log-cpm values from limma
limma edgeR RNASeq
updated 12 days ago by 50k • written 13 days ago by • 0
2
votes
3
replies
363
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
2
votes
1
reply
299
views
removeBatchEffect with non-linear model fit
limma DESeq2
updated 4 months ago by 50k • written 4 months ago by • 0
0
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2
replies
1.4k
views
Calculation of t-tests for factorial design
Microarray limma Microarray limma
written 13.6 years ago by ▴ 80
0
votes
2
replies
192
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
12 days ago • updated 9 days ago catv • 0
1
vote
1
reply
359
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 7 months ago by 65k • written 7 months ago by ▴ 10
0
votes
3
replies
415
views
Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip limma goana
updated 4 months ago by ▴ 350 • written 4 months ago by • 0
5
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2
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684
views
PhD student
TMM limma
10 months ago Nisha • 0
1
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6
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1.7k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 8 months ago by 50k • written 3.6 years ago by ▴ 20
5
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5
replies
790
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
8 months ago Jitendra ▴ 10
1
vote
4
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721
views
Pairwise differential expression using limma
limma
10 months ago Melissa • 0
0
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9
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549
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limma fo continous variables
limma DEGseq
updated 9 weeks ago by 65k • written 10 weeks ago by • 0
2
votes
4
replies
601
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
1
vote
3
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639
views
Can CAMERA analyze just one particular pathway
pathway ORA limma CAMERA DGE
updated 8 months ago by 50k • written 8 months ago by • 0
0
votes
1
reply
497
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
0
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2
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252
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Pairwise analysis of DESeq result and limma result
DESeq2 limma
12 weeks ago Lily Cheang ▴ 10
50 results • Page 1 of 1
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Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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