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rstudio
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DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 12 days ago by
swbarnes2
★ 1.3k • written 14 days ago by
Aaliya
• 0
0
votes
0
replies
238
views
RN to EC Mapping Not Working for Some Nodes
RStudio
ggkegg
updated 4 months ago by
James W. MacDonald
65k • written 4 months ago by
Ramirj49
• 0
2
votes
3
replies
504
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio
cDNA
ensembldb
NCBI
5 months ago
R_Page
• 0
0
votes
2
replies
376
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio
plotPCA
DESeq2
5 months ago
yee
• 0
1
vote
3
replies
468
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo
OrgDb
convert
Organismname
RStudio
updated 5 months ago by
James W. MacDonald
65k • written 6 months ago by
j_denton
• 0
2
votes
5
replies
809
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio
convert
ensembldb
NCBI
6 months ago
j_denton
• 0
0
votes
7
replies
1.6k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error
RStudio
ggplot2
DESeq2
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
BioES
• 0
0
votes
1
reply
389
views
FALSE error when checking a pre made sample data
Rstudio
scRNAseq
DESeq2
updated 9 months ago by
ATpoint
★ 4.1k • written 9 months ago by
DrFizz
• 0
0
votes
1
reply
1.0k
views
DESeq2 error after installing BiocManager
scRNAseq
RStudio
DESeq2
updated 9 months ago by
ATpoint
★ 4.1k • written 9 months ago by
DrFizz
• 0
9
votes
11
replies
5.9k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 8 weeks ago by
shepherl
3.9k • written 2.3 years ago by
jon.klonowski
▴ 40
10 results • Page
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Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
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