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pre-ranked GSEA within R? + Best DESeq2/limma-voom
limma edgeR limma edgeR
10.3 years ago Gordon Smyth 50k
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1
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3.2k
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GLM common and trended dispersion EdgeR
edgeR edgeR
updated 10.3 years ago by ▴ 570 • written 10.4 years ago by 50k
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593
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Question about best analysis method for a complex array experiment design
limma limma
10.4 years ago Gordon Smyth 50k
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3
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1.3k
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EdgeR glm based analysis
edgeR edgeR
10.4 years ago • updated 9 months ago Gordon Smyth 50k
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1.7k
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EdgeR Design matrix not of full rank. The following coefficients not estimable errorR
Regression edgeR Regression edgeR
10.4 years ago Gordon Smyth 50k
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866
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edgeR complex partial multifactorial design
edgeR edgeR
10.4 years ago Gordon Smyth 50k
0
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1
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3.0k
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EdgeR Design matrix not of full rank. The following coefficients not estimable errorR
edgeR edgeR
updated 10.4 years ago by ▴ 20 • written 10.4 years ago by 50k
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0
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579
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edgeR question (reading tab delimited files)
edgeR edgeR
10.4 years ago Gordon Smyth 50k
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0
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693
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Why the resuts are so different between the classic and the glm methods?
edgeR edgeR
10.4 years ago Gordon Smyth 50k
0
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0
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637
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Why the resuts are so different between the classic and the glm methods?
edgeR edgeR
10.4 years ago Gordon Smyth 50k
0
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1
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1.4k
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges Rsubread easyRNASeq GO
updated 10.5 years ago by ▴ 320 • written 10.5 years ago by 50k
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857
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limma - genas: unexpected warnings
limma limma
10.5 years ago Gordon Smyth 50k
0
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3
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1.4k
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edgeR on ncRNA analysis question
Normalization edgeR Normalization edgeR
updated 10.5 years ago by ▴ 330 • written 10.5 years ago by 50k
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1.7k
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question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray limma DOSE Microarray limma DOSE
10.5 years ago Gordon Smyth 50k
0
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0
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509
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Using changeLog() to see updates to limma package
limma limma
10.5 years ago Gordon Smyth 50k
0
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0
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608
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Separate channel analysis of two color micro arrays:avereps and intraspotCorrelation functions
limma limma
10.5 years ago Gordon Smyth 50k
0
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0
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1.0k
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Problem with topTable function (after Bioconductor update)
10.5 years ago Gordon Smyth 50k
0
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0
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1.3k
views
enrichment packages that accept t-stat (or related stat) as input
Microarray limma Category CAMERA GSVA Microarray limma Category CAMERA GSVA
10.6 years ago Gordon Smyth 50k
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0
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687
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select CPM value and what does logFC value mean_edgeR
10.6 years ago Gordon Smyth 50k
0
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2
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3.5k
views
limma: paired + multiple comparisons + technical replication?
limma limma
updated 10.6 years ago by ▴ 80 • written 10.6 years ago by 50k
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1
reply
1.5k
views
Can I input ordinal variables into a model in Limma?
Microarray limma Microarray limma
updated 10.7 years ago by ▴ 130 • written 10.7 years ago by 50k
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0
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1.5k
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microarray outlier detection
Microarray limma Microarray limma
10.7 years ago Gordon Smyth 50k
0
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0
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580
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EdgeR
edgeR edgeR
10.7 years ago Gordon Smyth 50k
0
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0
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774
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confusing P-value of one gene
edgeR edgeR
10.7 years ago Gordon Smyth 50k
2
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0
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2.0k
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Complex Limma design: technical replication, biological replication and repeated experiment
Microarray limma Microarray limma
10.7 years ago Gordon Smyth 50k
0
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0
replies
1.4k
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EdgeR annotation
Annotation edgeR Annotation edgeR
10.7 years ago Gordon Smyth 50k
0
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0
replies
810
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Vector for Targest in Tquantile Normalization for different groups
Microarray Normalization Microarray Normalization
10.8 years ago Gordon Smyth 50k
0
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0
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1.1k
views
edgeR: very low p-value and very high variance within the group of replicates
limma PROcess edgeR limma PROcess edgeR
10.9 years ago Gordon Smyth 50k
1
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4
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6.5k
views
How is LIMMA actually calculating the average expression value
probe limma gcrma probe limma gcrma
updated 10.9 years ago by ▴ 150 • written 10.9 years ago by 50k
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0
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690
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Huge variation in results among contrasts - Please Help!
10.9 years ago Gordon Smyth 50k
0
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0
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2.9k
views
Filtering is not recommended with LIMMA?
Microarray Preprocessing limma Microarray Preprocessing limma
11.0 years ago Gordon Smyth 50k
0
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2
replies
1.4k
views
Differential expression testing for groups with unequal variances/dispersions?
edgeR edgeR
updated 11.0 years ago by ★ 7.9k • written 11.0 years ago by 50k
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0
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941
views
RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq edgeR Rsubread Sequencing RNASeq edgeR Rsubread
11.0 years ago Gordon Smyth 50k
0
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0
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1.3k
views
How do I background correct an Illumina eset without using lumiB
Microarray probe limma PROcess convert beadarray lumi Microarray probe limma PROcess
11.0 years ago Gordon Smyth 50k
0
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0
replies
1.1k
views
problem with contrast.matrix and eBayes in limma
Microarray Microarray
11.0 years ago Gordon Smyth 50k
0
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0
replies
1.0k
views
Combining differential gene expression on 2 reference transcriptomes: EdgeR analysis
edgeR edgeR
11.0 years ago Gordon Smyth 50k
0
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1
reply
1.3k
views
calcNormFactors in edgeR - quick question from a very inexperienced user
Normalization edgeR Normalization edgeR
updated 11.0 years ago by ▴ 20 • written 11.0 years ago by 50k
0
votes
6
replies
1.6k
views
Design matrix and BCV
GO edgeR GO edgeR
updated 11.0 years ago by ▴ 110 • written 11.0 years ago by 50k
0
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0
replies
1.2k
views
Agilent 8x60K Gene Expression Package
Microarray Normalization limma Microarray Normalization limma
11.0 years ago Gordon Smyth 50k
0
votes
1
reply
748
views
Limma/Affy - Include expression Intensity in Final 'decideTests' results
Annotation limma Annotation limma
updated 11.0 years ago by ▴ 310 • written 11.0 years ago by 50k
0
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0
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1.1k
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edgeR: Using ratios (translational efficiencies) as input
RNASeq GO limma edgeR RNASeq GO limma edgeR
11.1 years ago Gordon Smyth 50k
0
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0
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803
views
edgeR asimmetry in miRNA experiment
miRNA Cancer edgeR miRNA Cancer edgeR
11.1 years ago Gordon Smyth 50k
0
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1
reply
738
views
Differences between lmfit model(from limma package) and Illumina-custom Model (from GenomeStudio)
probe limma probe limma
11.1 years ago Gordon Smyth 50k
0
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5
replies
1.2k
views
lmFit not keeping rownames of arg object?
limma limma
updated 11.1 years ago by ▴ 70 • written 11.1 years ago by 50k
0
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0
replies
709
views
edgeR : Include or exclude structural/noncoding RNA reads in the analysis
RNASeq edgeR RNASeq edgeR
11.1 years ago Gordon Smyth 50k
0
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0
replies
1.3k
views
lmFit() with ExpressionSet
Annotation probe limma Annotation probe limma
11.1 years ago Gordon Smyth 50k
0
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0
replies
754
views
Running new and old versions of edgeR concurrently
edgeR edgeR
11.2 years ago Gordon Smyth 50k
0
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1
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1.6k
views
Limma: difficulties making multiple comparisons within one multiple-group model
limma limma
updated 11.2 years ago by ▴ 130 • written 11.2 years ago by 50k
0
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0
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1.5k
views
Normalization
Normalization edgeR Normalization edgeR
11.2 years ago Gordon Smyth 50k
0
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0
replies
1.8k
views
AgiMicroRna for new Agilent Chip format
Microarray GO limma PROcess microRNA AgiMicroRna Microarray GO limma PROcess microRNA
11.2 years ago Gordon Smyth 50k
679 results • Page 2 of 14
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