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Showing :
Deseq2
•
reset
2
votes
5
replies
281
views
Differential variability modelling with vst() expression
limma
DESeq2
written 10 days ago by
jtsy6383
• 0
0
votes
2
replies
340
views
DESeq2 analysis with transcript counts
Transcriptomics
RNASeq
DESeq2
11 days ago • updated 8 days ago
sindhuri
• 0
2
votes
9
replies
703
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2
BatchEffect
updated 4 days ago by
Michael Love
43k • written 11 days ago by
Quang
▴ 10
1
vote
1
reply
269
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond
DESeq2
rnaseqDTU
updated 12 days ago by
Michael Love
43k • written 12 days ago by
muhammadsohailraza
• 0
0
votes
1
reply
147
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 13 days ago by
swbarnes2
★ 1.4k • written 13 days ago by
natalievillafranca
• 0
0
votes
1
reply
331
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR
DESeq2
updated 16 days ago by
Michael Love
43k • written 27 days ago by
Jimmy Mak
• 0
2
votes
1
reply
335
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2
RNASeqData
updated 16 days ago by
Michael Love
43k • written 24 days ago by
KR
• 0
0
votes
2
replies
251
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
22 days ago • updated 20 days ago
Kucsera
• 0
1
vote
1
reply
363
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 4 weeks ago by
Michael Love
43k • written 5 weeks ago by
txema.heredia
• 0
1
vote
9
replies
801
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma
DESeq2
edgeR
written 4 weeks ago by
anna.cot.anna.cot
▴ 30
0
votes
2
replies
303
views
Standardization of rlog transformed counts before PCA
RNASeq
DESeq2
Visualization
updated 4 weeks ago by
ATpoint
★ 4.6k • written 5 weeks ago by
bbao
• 0
1
vote
5
replies
555
views
Deseq2 Design
RNASeq
DESeq2
updated 4 weeks ago by
James W. MacDonald
67k • written 5 weeks ago by
pm_25
• 0
0
votes
5
replies
499
views
p value is 0, padj is 0
DESeq2
5 weeks ago
Wirayatida
• 0
1
vote
2
replies
479
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
5 weeks ago
georgii.vdovin
• 0
0
votes
7
replies
791
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 5 weeks ago by
txema.heredia
• 0 • written 5 weeks ago by
fjrsa
• 0
0
votes
1
reply
273
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 6 weeks ago by
Michael Love
43k • written 6 weeks ago by
bhandary.8590
▴ 20
0
votes
3
replies
408
views
DESeq2 - Comparing Comparisons
DESeq2
updated 5 weeks ago by
James W. MacDonald
67k • written 6 weeks ago by
sk
• 0
0
votes
4
replies
534
views
lfcShrink and alpha value
lfcShrink
DESeq2
7 weeks ago • updated 6 weeks ago
cropero
• 0
1
vote
1
reply
278
views
DESeq2- merging technical vs biological replicates
DESeq2
RNASeqData
updated 6 weeks ago by
Michael Love
43k • written 7 weeks ago by
Nikita
• 0
0
votes
2
replies
212
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates
DESeq2
updated 6 weeks ago by
Michael Love
43k • written 6 weeks ago by
Sam
• 0
0
votes
2
replies
262
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
7 weeks ago
Anna
• 0
1
vote
2
replies
554
views
Deseq2 res Function
DESeq2
updated 7 weeks ago by
James W. MacDonald
67k • written 8 weeks ago by
sap275
▴ 10
0
votes
4
replies
425
views
Help with RSEM counts: do I transpose matrix?
RSEM
DESeq2
8 weeks ago
NB
• 0
0
votes
5
replies
445
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 8 weeks ago by
Michael Love
43k • written 8 weeks ago by
maripane
• 0
0
votes
1
reply
250
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 8 weeks ago by
James W. MacDonald
67k • written 8 weeks ago by
rj1435
• 0
1
vote
2
replies
309
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
8 weeks ago
Denise
• 0
0
votes
1
reply
167
views
eRNAs count
RNASeq
DESeq2
updated 8 weeks ago by
ATpoint
★ 4.6k • written 8 weeks ago by
Irene
• 0
0
votes
1
reply
403
views
DESeq2 rerun returns different results
DESeq2
updated 9 weeks ago by
ATpoint
★ 4.6k • written 9 weeks ago by
wl1111
• 0
0
votes
1
reply
255
views
Is my time course analysis with DESeq2 valid?
GeneExpression
DESeq2
TimeCourse
updated 9 weeks ago by
Michael Love
43k • written 9 weeks ago by
Jason
• 0
0
votes
1
reply
242
views
DESeq2 "Not full rank" and "less than full rank" error
DESeq2
deseq
updated 9 weeks ago by
Guido Hooiveld
★ 4.1k • written 9 weeks ago by
Najla Abassi
• 0
2
votes
2
replies
639
views
Handling biological replicates in DESeq2
DESeq2
updated 9 weeks ago by
ATpoint
★ 4.6k • written 9 weeks ago by
sk
• 0
5
votes
2
replies
26k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
written 6.0 years ago by
aishu.jp
▴ 30
1
vote
6
replies
1.0k
views
Volcano plot has many values around zero
RNA-seq
DESeq2
volcanoplot
updated 10 weeks ago by
Michael Love
43k • written 10 weeks ago by
nramakr
▴ 10
0
votes
2
replies
392
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 10 weeks ago by
ballackselma
• 0
4
votes
5
replies
678
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
10 weeks ago
LuciaNhu
• 0
0
votes
1
reply
412
views
Average expression of genes across replicates
DESeq2
updated 11 weeks ago by
ATpoint
★ 4.6k • written 11 weeks ago by
James
• 0
0
votes
0
replies
150
views
News:
RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2
GenomicRanges
11 weeks ago
info
▴ 10
0
votes
10
replies
1.4k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
11 weeks ago • updated 10 weeks ago
Denise
• 0
0
votes
1
reply
365
views
Deseq to output continous sequencing data
DESeq2
updated 11 weeks ago by
Michael Love
43k • written 3 months ago by
Neha
• 0
1
vote
4
replies
868
views
Adjusted p-values become NA when sub-setting samples
DESeq2
3 months ago • updated 10 weeks ago
txema.heredia
• 0
3
votes
3
replies
946
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 12 weeks ago by
Satoshi
• 0
0
votes
2
replies
375
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2
ESTIMATE
RNASeqData
MCPcounter
written 12 weeks ago by
Aleksandra
• 0
0
votes
1
reply
322
views
Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
nicolettacommins
• 0
2
votes
3
replies
1.1k
views
Analysis of large RNA-Seq Datasets
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
KokiBio
• 0
1
vote
4
replies
798
views
DESeq2 - interactions when using factors concatenated into group
DESeq2
3 months ago • updated 12 weeks ago
boczniak767
▴ 740
0
votes
1
reply
231
views
2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
3 months ago
JY
• 0
0
votes
1
reply
309
views
How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
agamemnon
• 0
0
votes
2
replies
242
views
how to extract expression matrix post deseq2
DESeq2
written 3 months ago by
agamemnon
• 0
0
votes
2
replies
235
views
Using Normalized Counts in DESeq2
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
KokiBio
• 0
1
vote
2
replies
298
views
When running contrasts, does it use normalized read counts?
DESeq2
3 months ago
Katherine
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: EdgeR Biological CVs
by
Joseph
• 0
I believe the published study provides answers to your questions. Yunshun Chen and Pedro Baldoni's recent papers on edgeR may also be of in…
Answer: EdgeR Biological CVs
by
Gordon Smyth
52k
I think your questions are answered by the published paper. You might also like to consult recent papers on edgeR by Yunshun Chen and Pedro…
Answer: Curiously shaped volcano plot with using oarfish + swish to do differential gene
by
Michael Love
43k
See swish vignette, these are explained.
Comment: Problems with oarfish + tximport + swish
by
Michael Love
43k
Great thanks for posting the issue and sticking with it Annaleigh
Comment: Problems with oarfish + tximport + swish
by
brown.annaleigh
• 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
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