Showing : StatisticalMethod • reset
2
votes
2
replies
589
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
3 months ago Linton • 0
1
vote
2
replies
432
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
2
votes
2
replies
388
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
5 months ago Manthos • 0
4
votes
2
replies
590
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 5 months ago by 50k • written 5 months ago by ▴ 10
3
votes
2
replies
662
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 10 months ago by 50k • written 10 months ago by ▴ 10
2
votes
3
replies
1.8k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
2
votes
4
replies
730
views
Model comparison in mean-dispersion trend in DESeq2
DESeq2 StatisticalMethod
14 months ago Loïc • 0
0
votes
2
replies
721
views
Using Multi-Dimensional Scaling (MDS) to produce a vector in order to account for patient bias when constructing DGE lists from RNA-seq datasets in R?
PrincipalComponent StatisticalMethod edgeR MultidimensionalScaling Normalization
14 months ago rcreswell01 • 0
1
vote
3
replies
884
views
Limma-voom with inverse probability weights (similar to sample weights)
limma limma-voom StatisticalMethod
updated 14 months ago by 50k • written 14 months ago by • 0
0
votes
0
replies
606
views
Job: Academic position in Non-clinical Biostatistics
JobPosting StatisticalMethod
17 months ago Laurent Gatto 1.6k
0
votes
1
reply
525
views
DESeq2 paired multifactor test
DESeq2 StatisticalMethod
updated 17 months ago by 41k • written 18 months ago by ▴ 10
1
vote
2
replies
952
views
Limma adj.p.value the same for many different p.values
limmaGUI limma adj.p.value StatisticalMethod
19 months ago walkerrh95 • 0
0
votes
0
replies
869
views
Job: Postdoctoral research scientist in computational biology/statistical genetics/functional genomics at Columbia University, USA
Alzheimer's StatisticalMethod Genetics molecularQTL FunctionalGenomics
19 months ago gaow • 0
0
votes
0
replies
559
views
Should I adjust p value for multi-levels (groups) and multi-variables?
StatisticalMethod
2.1 years ago dong ▴ 10
2
votes
3
replies
3.1k
views
Differential gene expression and (adjusted) p-values
edgeR StatisticalMethod
updated 24 months ago by • 0 • written 2.2 years ago by • 0
6
votes
4
replies
974
views
Limma prametrization
limm MathematicalBiology limmaGUI StatisticalMethod
2.3 years ago Giovanni • 0
2
votes
7
replies
1.4k
views
EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on individual patients not combined
edgeR StatisticalMethod
2.6 years ago Field -Ye • 0
0
votes
2
replies
1.3k
views
To retrieve the transcript from gff file with the longest isoform
FunctionalAnnotation StatisticalMethod
2.8 years ago Aneesha • 0
0
votes
1
reply
729
views
DESeq2 Design matrix
StatisticalMethod DESeq2
updated 2.9 years ago by 41k • written 2.9 years ago by • 0
6
votes
6
replies
1.6k
views
limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 10
1
vote
3
replies
1.1k
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 3.2 years ago by 41k • written 3.2 years ago by • 0
0
votes
0
replies
1.2k
views
Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network StatisticalMethod WGCNA ExpressionData
3.3 years ago jol.espinoz ▴ 40
0
votes
2
replies
717
views
p adjusted value not available
StatisticalMethod DESeq2
updated 3.4 years ago by ★ 3.9k • written 3.4 years ago by • 0
23 results • Page 1 of 1
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Awards • All
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Popular Question to Bine ▴ 40
Locations • All
Germany, just now
France, 5 minutes ago
France, 12 minutes ago
Jerusalem, 13 minutes ago
France, 17 minutes ago
Traffic: 946 users visited in the last hour
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