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nanostringdiff
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0
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814
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fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
11 months ago
pg45863
▴ 10
0
votes
2
replies
839
views
Nanostring data differential expression analysis: limma or DESeq2?
DESeq2
NanoStringDiff
limma
11 months ago
pg45863
▴ 10
0
votes
1
reply
622
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
Aleksandra
• 0
0
votes
2
replies
509
views
NanoStringDiff contrast vectors
NanoStringDiff
updated 16 months ago by
James W. MacDonald
65k • written 16 months ago by
Paraskevi
• 0
0
votes
0
replies
544
views
NanoStringDiff
DifferentialExpression
NanoStringDiff
2.4 years ago
sanrie10
• 0
5
votes
7
replies
1.5k
views
Nanostringdiff - defining contrast values for blocking variables in glm
limma
edgeR
DESeq2
NanoStringDiff
updated 2.6 years ago by
James W. MacDonald
65k • written 2.6 years ago by
reberya
• 0
3
votes
2
replies
963
views
R NanoStringDiff: DE analysis, from 2 group comparison method how "logFC" generated?
Nan
NanoStringDiff
2.8 years ago
choijamts
• 0
0
votes
0
replies
651
views
NanoStringDiff - housekeeping genes variation
NanoStringDiff
3.1 years ago
YM
• 0
1
vote
1
reply
892
views
NanoStringDiff Not Recognized as Numeric
Bioconductor
Transcriptomics
NanoStringDiff
updated 3.5 years ago by
Laurent Gatto
1.6k • written 3.5 years ago by
Pedro
▴ 10
1
vote
7
replies
1.1k
views
NanoStringDiff glm.LRT not finishing after 20 hours
NanoStringDiff
4.3 years ago
stephen.pollo
• 0
0
votes
2
replies
865
views
NanoStringDiff correction for variation between patient
NanoStringDiff
GLM
Gene expression
updated 4.7 years ago by
James W. MacDonald
65k • written 4.7 years ago by
Guillaume Robert
• 0
3
votes
6
replies
1.9k
views
Why NanoStringDiff package so slow?
NanoStringDiff
NanoString
nCounter
DE analysis
updated 5 months ago by
georgersmith
• 0 • written 4.7 years ago by
lim6432
▴ 50
3
votes
3
replies
1.4k
views
NanoStringDiff counts not numeric
NanoStringDiff
updated 3 months ago by
pjanas
• 0 • written 4.9 years ago by
noelleenright
▴ 10
1
vote
6
replies
1.9k
views
How to access normalized data in the NanoStringDiff package?
nanostringdiff
nanostring
NanoStringDiff
updated 5.9 years ago by
James W. MacDonald
65k • written 5.9 years ago by
casey.rimland
▴ 150
0
votes
0
replies
1.3k
views
design matrix and contrast for paired experiment using NanoStringDiff for nCounter data
nanostring
NanoStringDiff
design and contrast matrix
differential gene expression
ncounter
6.8 years ago
c.kohler
• 0
15 results • Page
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Answer: get BM error
by
James W. MacDonald
65k
The genes you present are orthologous mappings from D. rerio to other teleost fishes, so it is probably going to be difficult to map to NCB…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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