Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
Showing : questions
0
votes
0
replies
2.7k
views
pre-ranked GSEA within R? + Best DESeq2/limma-voom
limma edgeR limma edgeR
10.3 years ago Gordon Smyth 50k
0
votes
1
reply
3.1k
views
GLM common and trended dispersion EdgeR
edgeR edgeR
updated 10.3 years ago by ▴ 570 • written 10.3 years ago by 50k
0
votes
0
replies
590
views
Question about best analysis method for a complex array experiment design
limma limma
10.3 years ago Gordon Smyth 50k
0
votes
3
replies
1.2k
views
EdgeR glm based analysis
edgeR edgeR
10.3 years ago • updated 8 months ago Gordon Smyth 50k
0
votes
0
replies
1.7k
views
EdgeR Design matrix not of full rank. The following coefficients not estimable errorR
Regression edgeR Regression edgeR
10.3 years ago Gordon Smyth 50k
0
votes
0
replies
858
views
edgeR complex partial multifactorial design
edgeR edgeR
10.3 years ago Gordon Smyth 50k
0
votes
1
reply
3.0k
views
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
0
votes
0
replies
575
views
edgeR question (reading tab delimited files)
edgeR edgeR
10.4 years ago Gordon Smyth 50k
0
votes
0
replies
690
views
Why the resuts are so different between the classic and the glm methods?
edgeR edgeR
10.4 years ago Gordon Smyth 50k
0
votes
0
replies
621
views
Why the resuts are so different between the classic and the glm methods?
edgeR edgeR
10.4 years ago Gordon Smyth 50k
0
votes
1
reply
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 10.4 years ago by ▴ 320 • written 10.4 years ago by 50k
0
votes
0
replies
851
views
limma - genas: unexpected warnings
limma limma
10.4 years ago Gordon Smyth 50k
0
votes
3
replies
1.4k
views
edgeR on ncRNA analysis question
Normalization edgeR Normalization edgeR
updated 10.4 years ago by ▴ 330 • written 10.4 years ago by 50k
0
votes
0
replies
1.7k
views
question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray limma DOSE Microarray limma DOSE
10.4 years ago Gordon Smyth 50k
0
votes
0
replies
503
views
Using changeLog() to see updates to limma package
limma limma
10.5 years ago Gordon Smyth 50k
0
votes
0
replies
604
views
Separate channel analysis of two color micro arrays:avereps and intraspotCorrelation functions
limma limma
10.5 years ago Gordon Smyth 50k
0
votes
0
replies
1.0k
views
Problem with topTable function (after Bioconductor update)
10.5 years ago Gordon Smyth 50k
0
votes
0
replies
1.3k
views
enrichment packages that accept t-stat (or related stat) as input
Microarray limma Category CAMERA GSVA Microarray limma Category CAMERA GSVA
10.5 years ago Gordon Smyth 50k
0
votes
0
replies
683
views
select CPM value and what does logFC value mean_edgeR
10.5 years ago Gordon Smyth 50k
0
votes
2
replies
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
0
votes
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
0
votes
0
replies
1.5k
views
microarray outlier detection
Microarray limma Microarray limma
10.7 years ago Gordon Smyth 50k
0
votes
0
replies
578
views
EdgeR
edgeR edgeR
10.7 years ago Gordon Smyth 50k
0
votes
0
replies
768
views
confusing P-value of one gene
edgeR edgeR
10.7 years ago Gordon Smyth 50k
2
votes
0
replies
2.0k
views
Complex Limma design: technical replication, biological replication and repeated experiment
Microarray limma Microarray limma
10.7 years ago Gordon Smyth 50k
0
votes
0
replies
1.4k
views
EdgeR annotation
Annotation edgeR Annotation edgeR
10.7 years ago Gordon Smyth 50k
0
votes
0
replies
804
views
Vector for Targest in Tquantile Normalization for different groups
Microarray Normalization Microarray Normalization
10.8 years ago Gordon Smyth 50k
0
votes
0
replies
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
vote
4
replies
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
0
votes
0
replies
682
views
Huge variation in results among contrasts - Please Help!
10.9 years ago Gordon Smyth 50k
0
votes
0
replies
2.8k
views
Filtering is not recommended with LIMMA?
Microarray Preprocessing limma Microarray Preprocessing limma
10.9 years ago Gordon Smyth 50k
0
votes
2
replies
1.4k
views
Differential expression testing for groups with unequal variances/dispersions?
edgeR edgeR
updated 10.9 years ago by ★ 7.9k • written 10.9 years ago by 50k
0
votes
0
replies
934
views
RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq edgeR Rsubread Sequencing RNASeq edgeR Rsubread
10.9 years ago Gordon Smyth 50k
0
votes
0
replies
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
10.9 years ago Gordon Smyth 50k
0
votes
0
replies
1.1k
views
problem with contrast.matrix and eBayes in limma
Microarray Microarray
11.0 years ago Gordon Smyth 50k
0
votes
0
replies
999
views
Combining differential gene expression on 2 reference transcriptomes: EdgeR analysis
edgeR edgeR
11.0 years ago Gordon Smyth 50k
0
votes
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
votes
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
741
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
votes
0
replies
1.1k
views
edgeR: Using ratios (translational efficiencies) as input
RNASeq GO limma edgeR RNASeq GO limma edgeR
11.0 years ago Gordon Smyth 50k
0
votes
0
replies
798
views
edgeR asimmetry in miRNA experiment
miRNA Cancer edgeR miRNA Cancer edgeR
11.0 years ago Gordon Smyth 50k
0
votes
1
reply
734
views
Differences between lmfit model(from limma package) and Illumina-custom Model (from GenomeStudio)
probe limma probe limma
11.0 years ago Gordon Smyth 50k
0
votes
5
replies
1.2k
views
lmFit not keeping rownames of arg object?
limma limma
updated 11.0 years ago by ▴ 70 • written 11.0 years ago by 50k
0
votes
0
replies
705
views
edgeR : Include or exclude structural/noncoding RNA reads in the analysis
RNASeq edgeR RNASeq edgeR
11.1 years ago Gordon Smyth 50k
0
votes
0
replies
1.3k
views
lmFit() with ExpressionSet
Annotation probe limma Annotation probe limma
11.1 years ago Gordon Smyth 50k
0
votes
0
replies
751
views
Running new and old versions of edgeR concurrently
edgeR edgeR
11.2 years ago Gordon Smyth 50k
0
votes
1
reply
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
votes
0
replies
1.4k
views
Normalization
Normalization edgeR Normalization edgeR
11.2 years ago Gordon Smyth 50k
0
votes
0
replies
1.7k
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
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6