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Showing :
matrix
•
reset
1
vote
2
replies
487
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq
Design
Matrix
14 months ago
Barista
• 0
3
votes
7
replies
841
views
small dimensions in the matrix of counts from smallRNA using DESEq2
matrix
DESeq2
SmallRNA
dimensions
small
17 months ago
andreia
▴ 10
2
votes
3
replies
655
views
Differential expression error in edgeR - maybe from design matrix?
design
edgeR
matrix
RNA-seq
MDplot
updated 20 months ago by
Gordon Smyth
47k • written 20 months ago by
Alex
• 0
1
vote
2
replies
470
views
How to construct matrix and fit linear model for this microarray?
microarray
dge
matrix
makecontrasts
limma
updated 2.6 years ago by
Gordon Smyth
47k • written 2.6 years ago by
June.
▴ 10
4
votes
8
replies
771
views
problem in designing matrix and batch effect
edger
rna-seq
matrix
updated 3.1 years ago by
James W. MacDonald
62k • written 3.1 years ago by
alihakimzadeh73
• 0
2
votes
3
replies
793
views
Filtering counts in SummarizedExperiment
diffbind
matrix
summarizedexperiment
rangedCounts
updated 3.3 years ago by
Rory Stark
★ 4.6k • written 3.3 years ago by
rbronste
▴ 60
3
votes
7
replies
1.9k
views
Handle missing values in the z-score matrix while plotting heatmap in the ComplexHeatmap
matrix
heatmap
ComplexHeatmap
missing values
R
updated 3.4 years ago by
Zuguang Gu
▴ 240 • written 3.4 years ago by
mohammedtoufiq91
▴ 10
2
votes
4
replies
612
views
Are there any functions to subtract all features(rows) to a particular value(row) in the same data file?
R
python
normalization
matrix
updated 3.5 years ago by
shahryary
▴ 30 • written 3.5 years ago by
mohammedtoufiq91
▴ 10
3
votes
1
reply
1.3k
views
Convert Flowframe to matrix
flowcore
fcs
flow cytommetry
matrix
conversion
updated 3.6 years ago by
Jake Wagner
▴ 310 • written 3.6 years ago by
apurva
• 0
3
votes
4
replies
839
views
Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger
design
matrix
de
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
takumima
▴ 10
1
vote
2
replies
556
views
want the piece of the matrix I wanted
matrix
updated 4.6 years ago by
Axel Klenk
▴ 990 • written 4.6 years ago by
yueli7
▴ 20
0
votes
5
replies
815
views
DESeq2 design formula - correlation with ordered variable
DESeq2
design
formula
matrix
updated 4.7 years ago by
Michael Love
39k • written 4.7 years ago by
t.kuilman
170
3
votes
2
replies
489
views
Scoring a seq based on a matrix
matrix
updated 4.7 years ago by
Martin Morgan
25k • written 4.7 years ago by
ahmad.iut
• 0
10
votes
7
replies
1.6k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery
summarizedexperiment
GEO
matrix
updated 5.1 years ago by
Sean Davis
21k • written 5.1 years ago by
rbronste
▴ 60
0
votes
7
replies
1.8k
views
Deseq2 no package Matrix found
deseq2
bioconductor
matrix
5.4 years ago • updated 5.3 years ago
victoria.carla.moris
• 0
3
votes
8
replies
2.0k
views
S4Vectors masks/breaks regular Matrix functions
S4Vectors
Matrix
6.0 years ago
peter.kharchenko
▴ 30
3
votes
2
replies
1.3k
views
DEXSeq throws a warning - rank-deficient matrix
dexseq
fit
matrix
warning
updated 14 months ago by
koushik
• 0 • written 6.0 years ago by
Assa Yeroslaviz
★ 1.5k
1
vote
2
replies
904
views
sva :: sva can variable of interest be a matrix itself?
sva
variable of ineterest
matrix
updated 6.2 years ago by
Jeff Leek
▴ 640 • written 6.2 years ago by
reyhan.sonmez
• 0
0
votes
1
reply
585
views
[General] compare matrix to vector higher/lower
matrix
updated 7.4 years ago by
andrew.j.skelton73
▴ 360 • written 7.4 years ago by
BenAbflack
• 0
1
vote
3
replies
1.7k
views
[DiffBind] Memory issues with dba.count()
diffbind
bigmemory
matrix
dba.count
updated 7.5 years ago by
Rory Stark
★ 4.6k • written 7.5 years ago by
enricoferrero
▴ 650
0
votes
4
replies
1.2k
views
reading in data and transform it to matrix format
matrix
text
7.6 years ago
Angel
▴ 40
21 results • Page
1 of 1
Recent ...
Replies
Answer: struggling to create a heatmap
by
ATpoint
★ 2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta
by
Michael Love
39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
by
ATpoint
★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2?
by
ATpoint
★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2?
by
Michael Love
39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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