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DESeq2
•
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0
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0
replies
14
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
6 hours ago
bhandary.8590
▴ 20
0
votes
1
reply
116
views
DESeq2 - Comparing Comparisons
DESeq2
updated 2 days ago by
James W. MacDonald
67k • written 2 days ago by
sk
• 0
0
votes
4
replies
279
views
lfcShrink and alpha value
lfcShrink
DESeq2
7 days ago • updated 2 days ago
cropero
• 0
1
vote
1
reply
168
views
DESeq2- merging technical vs biological replicates
DESeq2
RNASeqData
updated 4 days ago by
Michael Love
43k • written 11 days ago by
Nikita
• 0
0
votes
2
replies
106
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates
DESeq2
updated 4 days ago by
Michael Love
43k • written 4 days ago by
Sam
• 0
0
votes
2
replies
156
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
10 days ago • updated 9 days ago
Anna
• 0
1
vote
2
replies
453
views
Deseq2 res Function
DESeq2
updated 11 days ago by
James W. MacDonald
67k • written 13 days ago by
sap275
▴ 10
0
votes
4
replies
348
views
Help with RSEM counts: do I transpose matrix?
RSEM
DESeq2
14 days ago
NB
• 0
0
votes
5
replies
325
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 14 days ago by
Michael Love
43k • written 15 days ago by
maripane
• 0
0
votes
1
reply
192
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 15 days ago by
James W. MacDonald
67k • written 15 days ago by
rj1435
• 0
1
vote
2
replies
244
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
16 days ago • updated 15 days ago
Denise
• 0
0
votes
1
reply
115
views
eRNAs count
RNASeq
DESeq2
updated 18 days ago by
ATpoint
★ 4.6k • written 18 days ago by
Irene
• 0
0
votes
1
reply
369
views
DESeq2 rerun returns different results
DESeq2
updated 21 days ago by
ATpoint
★ 4.6k • written 21 days ago by
wl1111
• 0
0
votes
1
reply
201
views
Is my time course analysis with DESeq2 valid?
GeneExpression
DESeq2
TimeCourse
updated 22 days ago by
Michael Love
43k • written 23 days ago by
Jason
• 0
0
votes
1
reply
168
views
DESeq2 "Not full rank" and "less than full rank" error
DESeq2
deseq
updated 24 days ago by
Guido Hooiveld
★ 4.1k • written 24 days ago by
Najla Abassi
• 0
2
votes
2
replies
553
views
Handling biological replicates in DESeq2
DESeq2
updated 24 days ago by
ATpoint
★ 4.6k • written 25 days ago by
sk
• 0
5
votes
2
replies
25k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
written 5.9 years ago by
aishu.jp
▴ 30
1
vote
6
replies
907
views
Volcano plot has many values around zero
RNA-seq
DESeq2
volcanoplot
updated 28 days ago by
Michael Love
43k • written 28 days ago by
nramakr
▴ 10
0
votes
2
replies
344
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 4 weeks ago by
ballackselma
• 0
4
votes
5
replies
598
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
4 weeks ago
LuciaNhu
• 0
0
votes
1
reply
374
views
Average expression of genes across replicates
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.6k • written 5 weeks ago by
James
• 0
0
votes
0
replies
113
views
News:
RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2
GenomicRanges
5 weeks ago
info
▴ 10
0
votes
10
replies
1.3k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
5 weeks ago • updated 4 weeks ago
Denise
• 0
0
votes
1
reply
323
views
Deseq to output continous sequencing data
DESeq2
updated 5 weeks ago by
Michael Love
43k • written 8 weeks ago by
Neha
• 0
1
vote
4
replies
778
views
Adjusted p-values become NA when sub-setting samples
DESeq2
8 weeks ago • updated 4 weeks ago
txema.heredia
• 0
3
votes
3
replies
861
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 5 weeks ago by
Satoshi
• 0
0
votes
2
replies
334
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2
ESTIMATE
RNASeqData
MCPcounter
written 6 weeks ago by
Aleksandra
• 0
0
votes
1
reply
277
views
Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 6 weeks ago by
Michael Love
43k • written 6 weeks ago by
nicolettacommins
• 0
2
votes
3
replies
1.0k
views
Analysis of large RNA-Seq Datasets
DESeq2
updated 6 weeks ago by
Michael Love
43k • written 7 weeks ago by
KokiBio
• 0
1
vote
4
replies
734
views
DESeq2 - interactions when using factors concatenated into group
DESeq2
7 weeks ago • updated 6 weeks ago
boczniak767
▴ 740
0
votes
1
reply
190
views
2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
7 weeks ago
JY
• 0
0
votes
1
reply
273
views
How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 7 weeks ago by
Michael Love
43k • written 7 weeks ago by
agamemnon
• 0
0
votes
2
replies
200
views
how to extract expression matrix post deseq2
DESeq2
written 7 weeks ago by
agamemnon
• 0
0
votes
2
replies
202
views
Using Normalized Counts in DESeq2
DESeq2
updated 7 weeks ago by
Michael Love
43k • written 7 weeks ago by
KokiBio
• 0
1
vote
2
replies
245
views
When running contrasts, does it use normalized read counts?
DESeq2
7 weeks ago
Katherine
• 0
0
votes
1
reply
201
views
How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 7 weeks ago by
swbarnes2
★ 1.4k • written 8 weeks ago by
Bingqian
• 0
3
votes
4
replies
481
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization
DESeq2
rlog
vst
8 weeks ago
Eva
▴ 10
1
vote
4
replies
485
views
Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq
DESeq2
Oddresults
updated 7 weeks ago by
ATpoint
★ 4.6k • written 9 weeks ago by
Ricardo Iván
• 0
0
votes
1
reply
176
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression
ImpulseDE2
DESeq2
updated 8 weeks ago by
Michael Love
43k • written 8 weeks ago by
Jay
• 0
3
votes
11
replies
725
views
Highly DE genes but small count difference within conditions
RNASeq
DESeq2
RNASeqData
written 8 weeks ago by
bioshot.com
• 0
2
votes
4
replies
407
views
RNASeq Time Course Question
DESeq2
RNASeq
TimeCourse
8 weeks ago
jihoon.kim.1495
▴ 10
0
votes
6
replies
812
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression
DESeq2
BatchEffect
updated 5 weeks ago by
Michael Love
43k • written 8 weeks ago by
CriticalPeriod
• 0
5
votes
4
replies
446
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 8 weeks ago by
ATpoint
★ 4.6k • written 9 weeks ago by
Bioinformagician
• 0
0
votes
2
replies
280
views
RNA-Seq p value range variation
DESeq2
pvalue
RNA-Seq
9 weeks ago • updated 8 weeks ago
paul.meraner
• 0
0
votes
0
replies
189
views
News:
RNAseq data analysis with Bioconductor (online course)
DESeq2
SummarizedExperiment
8 weeks ago • updated 5 weeks ago
info
▴ 10
0
votes
5
replies
592
views
heatmap with batch effect
DESeq2
BatchEffect
9 weeks ago • updated 8 weeks ago
tothuhien
• 0
0
votes
2
replies
363
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport
DESeq2
updated 9 weeks ago by
Michael Love
43k • written 9 weeks ago by
oguzhankaraosmanoglu
• 0
1
vote
1
reply
276
views
Deseq2 sfType
Microbiome
DESeq2
RNASeq
updated 9 weeks ago by
James W. MacDonald
67k • written 9 weeks ago by
Caroline
• 0
1
vote
1
reply
239
views
Normalization RNA-seq for multiple plates
Normalization
DESeq2
RNASeqData
edgeR
updated 9 weeks ago by
ATpoint
★ 4.6k • written 9 weeks ago by
Pimpa
• 0
1
vote
1
reply
331
views
DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 9 weeks ago by
ATpoint
★ 4.6k • written 9 weeks ago by
picasa1983
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: sva: get a sv for RIN scores
by
gabriel.hoffman
▴ 170
Agreed. I'll add that with small sample size, a covariate can explain some fraction of expression variation even under the null.
Comment: RSubread output significantly different from bash Subread output
by
Aimee
• 0
Thank you! I will try rerunning with that parameter and see if it fixes the discrepancy! I'll report back. Update: This completely resolve…
Answer: RSubread output significantly different from bash Subread output
by
ATpoint
★ 4.6k
The R version counts multimappers (countMultiMappingReads is TRUE by default) while the command line version does not. It's beyond me why t…
Comment: Can't post a question?
by
Aimee
• 0
I copied my text to a file in linux and ran: ```r grep --color='auto' -P -n "[^\x00-\x7F]" filename.txt ``` It highlighted everything that…
Answer: sva: get a sv for RIN scores
by
Gordon Smyth
52k
Surrogate variables are not constructed from known variates, so one doesn't get surrogate variables for RIN scores. I am guessing that the …
Votes
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: How to annotate a limma Elist raw class object with an annotation file
Comment: How to annotate a limma Elist raw class object with an annotation file
QSEA- Extraction of Normalized methylation across the samples
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