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nanostringdiff
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1.8k
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fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
22 months ago
pg45863
▴ 10
0
votes
2
replies
1.5k
views
Nanostring data differential expression analysis: limma or DESeq2?
DESeq2
NanoStringDiff
limma
22 months ago
pg45863
▴ 10
0
votes
1
reply
935
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
Aleksandra
• 0
0
votes
2
replies
727
views
NanoStringDiff contrast vectors
NanoStringDiff
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
Paraskevi
• 0
0
votes
0
replies
787
views
NanoStringDiff
DifferentialExpression
NanoStringDiff
3.3 years ago
sanrie10
• 0
5
votes
7
replies
2.0k
views
Nanostringdiff - defining contrast values for blocking variables in glm
limma
edgeR
DESeq2
NanoStringDiff
updated 3.6 years ago by
James W. MacDonald
68k • written 3.6 years ago by
reberya
• 0
3
votes
2
replies
1.3k
views
R NanoStringDiff: DE analysis, from 2 group comparison method how "logFC" generated?
Nan
NanoStringDiff
3.8 years ago
choijamts
• 0
3
votes
6
replies
2.4k
views
Why NanoStringDiff package so slow?
NanoStringDiff
NanoString
nCounter
DE analysis
updated 17 months ago by
georgersmith
• 0 • written 5.7 years ago by
lim6432
▴ 50
0
votes
0
replies
866
views
NanoStringDiff - housekeeping genes variation
NanoStringDiff
4.0 years ago
YM
• 0
1
vote
1
reply
1.2k
views
NanoStringDiff Not Recognized as Numeric
Bioconductor
Transcriptomics
NanoStringDiff
updated 4.4 years ago by
Laurent Gatto
1.6k • written 4.4 years ago by
Pedro
▴ 10
1
vote
7
replies
1.4k
views
NanoStringDiff glm.LRT not finishing after 20 hours
NanoStringDiff
5.2 years ago
stephen.pollo
• 0
0
votes
2
replies
1.1k
views
NanoStringDiff correction for variation between patient
NanoStringDiff
GLM
Gene expression
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
Guillaume Robert
• 0
3
votes
3
replies
1.7k
views
NanoStringDiff counts not numeric
NanoStringDiff
updated 14 months ago by
pjanas
• 0 • written 5.9 years ago by
noelleenright
▴ 10
1
vote
6
replies
2.5k
views
How to access normalized data in the NanoStringDiff package?
nanostringdiff
nanostring
NanoStringDiff
updated 6.8 years ago by
James W. MacDonald
68k • written 6.8 years ago by
casey.rimland
▴ 170
0
votes
0
replies
1.6k
views
design matrix and contrast for paired experiment using NanoStringDiff for nCounter data
nanostring
NanoStringDiff
design and contrast matrix
differential gene expression
ncounter
7.7 years ago
c.kohler
• 0
15 results • Page
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Comment: DESeq2 - human data, weird results, troubleshooting
by
bd2000
▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
James W. MacDonald
68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
ATpoint
★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt
by
darylruiz6545
• 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash
by
Alex
• 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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