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NanoStringDiff
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1.9k
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fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
24 months ago • updated 23 months ago
pg45863
▴ 10
0
votes
2
replies
1.6k
views
Nanostring data differential expression analysis: limma or DESeq2?
DESeq2
NanoStringDiff
limma
24 months ago
pg45863
▴ 10
0
votes
1
reply
967
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
Aleksandra
• 0
0
votes
2
replies
742
views
NanoStringDiff contrast vectors
NanoStringDiff
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
Paraskevi
• 0
0
votes
0
replies
816
views
NanoStringDiff
DifferentialExpression
NanoStringDiff
3.4 years ago
sanrie10
• 0
5
votes
7
replies
2.1k
views
Nanostringdiff - defining contrast values for blocking variables in glm
limma
edgeR
DESeq2
NanoStringDiff
updated 3.7 years ago by
James W. MacDonald
68k • written 3.7 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
3.9 years ago
choijamts
• 0
3
votes
6
replies
2.4k
views
Why NanoStringDiff package so slow?
NanoStringDiff
NanoString
nCounter
DE analysis
updated 18 months ago by
georgersmith
• 0 • written 5.8 years ago by
lim6432
▴ 50
0
votes
0
replies
880
views
NanoStringDiff - housekeeping genes variation
NanoStringDiff
4.2 years ago
YM
• 0
1
vote
1
reply
1.2k
views
NanoStringDiff Not Recognized as Numeric
Bioconductor
Transcriptomics
NanoStringDiff
updated 4.6 years ago by
Laurent Gatto
1.6k • written 4.6 years ago by
Pedro
▴ 10
1
vote
7
replies
1.4k
views
NanoStringDiff glm.LRT not finishing after 20 hours
NanoStringDiff
5.3 years ago
stephen.pollo
• 0
0
votes
2
replies
1.1k
views
NanoStringDiff correction for variation between patient
NanoStringDiff
GLM
Gene expression
updated 5.7 years ago by
James W. MacDonald
68k • written 5.7 years ago by
Guillaume Robert
• 0
3
votes
3
replies
1.8k
views
NanoStringDiff counts not numeric
NanoStringDiff
updated 16 months ago by
pjanas
• 0 • written 6.0 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 7.0 years ago by
James W. MacDonald
68k • written 7.0 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
7.8 years ago
c.kohler
• 0
15 results • Page
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Comment: Check removeBatchEffect effectiveness
by
Gordon Smyth
52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data
by
sloperun3az
• 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash
by
sloperun3az
• 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr
by
Paul Harrison
▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Gordon Smyth
52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
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Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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