Showing : plotmds • reset
1
vote
2
replies
1.2k
views
loading scores using plotMDS in limma
plotMDS limma
15 months ago Cen • 0
1
vote
3
replies
3.2k
views
Making MDS plot
plotMDS limma
updated 16 months ago by 51k • written 16 months ago by • 0
2
votes
2
replies
1.6k
views
Make samples symbols bigger in PCA / MDS analysis with plotMDS function
plotMDS PCA RNASeq MDS
updated 2.6 years ago by 51k • written 2.6 years ago by ▴ 60
2
votes
2
replies
1.5k
views
plotMDS dimensions bug
limma plotMDS
3.3 years ago jamie.gearing ▴ 60
2
votes
8
replies
4.5k
views
MDS Plot help in edgeR
edgeR plotmds differential gene expression MDS mdsplot
updated 5.8 years ago by 51k • written 5.8 years ago by • 0
0
votes
1
reply
855
views
Visualization of analysis of multiple cell lines
plotMDS Cell lines limma
updated 6.2 years ago by 51k • written 6.2 years ago by ▴ 30
0
votes
0
replies
1.1k
views
Using log2FC distance matrix in Boot.Phylo to create bootstrapped trees
tree bootstrap dgelist plotmds
6.7 years ago Larry K. • 0
3
votes
7
replies
6.4k
views
Limma PlotMDS: what values should be used?
limma edger plotmds tmm masigpro
6.9 years ago dacaba.92 ▴ 10
4
votes
6
replies
1.8k
views
EdgeR: Replicate samples diverge in MDS plot
edger plotmds
7.1 years ago fawazfebin ▴ 60
3
votes
1
reply
2.2k
views
column nubering plotMDS
edger plotmds
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 10
1
vote
1
reply
1.8k
views
Inspection of batch effect correction success with ComBat in R, regarding a merged dataset comprised of 4 different batches
affymetrix microarrays sva combat sva batch effect plotMDS
updated 8.2 years ago by ▴ 650 • written 8.2 years ago by ▴ 830
0
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0
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1.3k
views
Is it possible to make some spheres around groups of points (plot3d) and measure distances between them?
rgl plot3d plotmds
8.6 years ago Adam • 0
12 results • Page 1 of 1
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Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0
Thank you!
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0
Hi Gordon, Thanks for the answer! This makes a lot of sense. Your suggested pipeline (separate processing of datasets -> gene set analyses…
Comment: How many of my genes from my gene list are in each KEGG pathway? by josephasmith1310 • 0
> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…
Comment: EuroBioC2024 abstract submission is open! by Esperan • 0
Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
Votes
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
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