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DeSeq2
•
reset
0
votes
2
replies
814
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
13 months ago
Kucsera
• 0
1
vote
1
reply
597
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
txema.heredia
• 0
1
vote
9
replies
1.7k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma
DESeq2
edgeR
written 13 months ago by
anna.cot.anna.cot
▴ 40
4
votes
2
replies
1.3k
views
Standardization of rlog transformed counts before PCA
RNASeq
DESeq2
Visualization
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
bbao
▴ 10
1
vote
5
replies
1.2k
views
Deseq2 Design
RNASeq
DESeq2
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
pm_25
• 0
0
votes
5
replies
1.3k
views
p value is 0, padj is 0
DESeq2
13 months ago
Wirayatida
• 0
1
vote
2
replies
1.3k
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
13 months ago
georgii.vdovin
• 0
0
votes
7
replies
1.4k
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 13 months ago by
txema.heredia
• 0 • written 13 months ago by
fjrsa
• 0
0
votes
1
reply
604
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
bhandary.8590
▴ 20
0
votes
3
replies
839
views
DESeq2 - Comparing Comparisons
DESeq2
updated 13 months ago by
James W. MacDonald
68k • written 14 months ago by
sk
• 0
0
votes
4
replies
1.0k
views
lfcShrink and alpha value
lfcShrink
DESeq2
14 months ago
anon
• 0
2
votes
1
reply
847
views
DESeq2- merging technical vs biological replicates
DESeq2
RNASeqData
updated 14 months ago by
Michael Love
43k • written 14 months ago by
Nikita
• 0
0
votes
2
replies
543
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates
DESeq2
updated 14 months ago by
Michael Love
43k • written 14 months ago by
Sam
• 0
0
votes
2
replies
544
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
14 months ago
Anna
• 0
1
vote
2
replies
857
views
Deseq2 res Function
DESeq2
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
sap275
▴ 10
0
votes
4
replies
818
views
Help with RSEM counts: do I transpose matrix?
RSEM
DESeq2
14 months ago
NB
• 0
0
votes
5
replies
816
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 14 months ago by
Michael Love
43k • written 14 months ago by
maripane
• 0
0
votes
1
reply
632
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
Raya
• 0
1
vote
2
replies
539
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
14 months ago
Denise
• 0
0
votes
1
reply
474
views
eRNAs count
RNASeq
DESeq2
updated 14 months ago by
ATpoint
★ 5.0k • written 14 months ago by
Irene
• 0
0
votes
1
reply
667
views
DESeq2 rerun returns different results
DESeq2
updated 14 months ago by
ATpoint
★ 5.0k • written 14 months ago by
wl1111
• 0
0
votes
1
reply
574
views
Is my time course analysis with DESeq2 valid?
GeneExpression
DESeq2
TimeCourse
updated 14 months ago by
Michael Love
43k • written 14 months ago by
Jason
• 0
0
votes
1
reply
711
views
DESeq2 "Not full rank" and "less than full rank" error
DESeq2
deseq
updated 14 months ago by
Guido Hooiveld
★ 4.1k • written 14 months ago by
Najla Abassi
• 0
2
votes
2
replies
1.2k
views
Handling biological replicates in DESeq2
DESeq2
updated 14 months ago by
ATpoint
★ 5.0k • written 14 months ago by
sk
• 0
5
votes
3
replies
29k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
written 7.1 years ago by
aishu.jp
▴ 30
1
vote
6
replies
1.7k
views
Volcano plot has many values around zero
RNA-seq
DESeq2
volcanoplot
updated 14 months ago by
Michael Love
43k • written 14 months ago by
nramakr
▴ 10
0
votes
2
replies
602
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 15 months ago by
ballackselma
• 0
4
votes
5
replies
1.5k
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
15 months ago
LuciaNhu
• 0
0
votes
1
reply
817
views
Average expression of genes across replicates
DESeq2
updated 15 months ago by
ATpoint
★ 5.0k • written 15 months ago by
James
• 0
0
votes
0
replies
470
views
News:
RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2
GenomicRanges
15 months ago
info
▴ 10
0
votes
11
replies
2.7k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 10 months ago by
Rob
• 0 • written 15 months ago by
Denise
• 0
0
votes
1
reply
587
views
Deseq to output continous sequencing data
DESeq2
updated 15 months ago by
Michael Love
43k • written 15 months ago by
Neha
• 0
1
vote
4
replies
1.5k
views
Adjusted p-values become NA when sub-setting samples
DESeq2
15 months ago • updated 14 months ago
txema.heredia
• 0
3
votes
3
replies
1.7k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 15 months ago by
Satoshi
• 0
0
votes
2
replies
1.0k
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2
ESTIMATE
RNASeqData
MCPcounter
written 15 months ago by
Aleksandra
• 0
0
votes
1
reply
518
views
Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 15 months ago by
Michael Love
43k • written 15 months ago by
nicolettacommins
• 0
2
votes
3
replies
1.4k
views
Analysis of large RNA-Seq Datasets
DESeq2
updated 15 months ago by
Michael Love
43k • written 15 months ago by
KokiBio
• 0
1
vote
4
replies
1.2k
views
DESeq2 - interactions when using factors concatenated into group
DESeq2
15 months ago
boczniak767
▴ 740
0
votes
1
reply
413
views
2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
15 months ago
JY
• 0
0
votes
1
reply
503
views
How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 15 months ago by
Michael Love
43k • written 15 months ago by
agamemnon
• 0
0
votes
2
replies
541
views
how to extract expression matrix post deseq2
DESeq2
written 15 months ago by
agamemnon
• 0
0
votes
2
replies
576
views
Using Normalized Counts in DESeq2
DESeq2
updated 15 months ago by
Michael Love
43k • written 15 months ago by
KokiBio
• 0
3
votes
2
replies
688
views
When running contrasts, does it use normalized read counts?
DESeq2
15 months ago
Katherine
▴ 20
0
votes
1
reply
451
views
How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 15 months ago by
swbarnes2
★ 1.4k • written 15 months ago by
Bingqian
• 0
3
votes
4
replies
1.5k
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization
DESeq2
rlog
vst
15 months ago
Eva
▴ 10
1
vote
4
replies
1.5k
views
Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq
DESeq2
Oddresults
updated 15 months ago by
ATpoint
★ 5.0k • written 16 months ago by
Ricardo Iván
• 0
0
votes
1
reply
565
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression
ImpulseDE2
DESeq2
updated 15 months ago by
Michael Love
43k • written 15 months ago by
Jiahao Tian
• 0
2
votes
4
replies
1.1k
views
RNASeq Time Course Question
DESeq2
RNASeq
TimeCourse
15 months ago
jihoon.kim.1495
▴ 10
0
votes
6
replies
1.5k
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression
DESeq2
BatchEffect
updated 15 months ago by
Michael Love
43k • written 15 months ago by
CriticalPeriod
• 0
5
votes
4
replies
1.1k
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 15 months ago by
ATpoint
★ 5.0k • written 16 months ago by
Bioinformagician
• 0
4,848 results • Page
3 of 97
Recent ...
Replies
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC
by
Ben
• 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis
by
James W. MacDonald
68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
varying.mastodon.isyn
• 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency)
by
Marina
• 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error
by
ansley.r.burtch
• 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Votes
A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
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