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Showing :
deseq
•
reset
1
vote
2
replies
314
views
evaluate the variable importance on genes
DESeq2
deseq
10 weeks ago • updated 9 weeks ago
Meme
• 0
0
votes
2
replies
335
views
Running DESeq on normalized data
deseq
DESeq2
updated 4 months ago by
ATpoint
★ 4.1k • written 4 months ago by
Hugo
• 0
2
votes
2
replies
520
views
Predicting missing values splines DESeq2
deseq
DESeq2
5 months ago
georgii.vdovin
• 0
0
votes
1
reply
381
views
Controling for Covariates With a Continuous Predictor Variable
Deseq
DESeq2
updated 5 months ago by
Michael Love
41k • written 5 months ago by
georgii.vdovin
• 0
0
votes
1
reply
651
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
khaserdene99
• 0
0
votes
3
replies
888
views
Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq
DESeq2
updated 9 months ago by
ATpoint
★ 4.1k • written 9 months ago by
Abir.khazaal
▴ 10
6
votes
11
replies
26k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq
deseq2
updated 9 months ago by
Erika
• 0 • written 9.3 years ago by
c.lieftink@nki.nl
▴ 40
0
votes
4
replies
657
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2
apeglm
DESeq
ApeGLM
Ashr
updated 9 months ago by
Michael Love
41k • written 9 months ago by
Ndimensional
▴ 20
2
votes
5
replies
5.6k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’
DESeq
written 4.1 years ago by
krunal.24.6
▴ 10
1
vote
2
replies
611
views
summarizeToGene in tximeta causing vastly different results
DESeq2
deseq
txime
tximeta
updated 12 months ago by
Michael Love
41k • written 12 months ago by
akrunic
• 0
0
votes
4
replies
1.2k
views
Volcano plot becomes flipped when I add a third condition
DESeq2
volcanoplot
deseq
HELP
contrast
updated 14 months ago by
Basti
▴ 780 • written 14 months ago by
Michael
• 0
0
votes
1
reply
566
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 15 months ago by
Michael Love
41k • written 15 months ago by
m-bihie
▴ 10
0
votes
1
reply
726
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 15 months ago by
Dario Strbenac
★ 1.5k • written 15 months ago by
Hicham
▴ 10
0
votes
1
reply
2.8k
views
voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)
Normalization
graph
limma
convert
edgeR
DESeq
Rsubread
Normalization
graph
limma
convert
updated 16 months ago by
Gordon Smyth
50k • written 11.9 years ago by
Kasper Daniel Hansen
★ 6.5k
0
votes
2
replies
1.2k
views
suggestions/comments on DESeq transcript wise analysis
convert
DESeq
convert
DESeq
written 12.2 years ago by
Akula, Nirmala NIH/NIMH [C]
▴ 190
1
vote
1
reply
520
views
How to design multifactor DESEQ2 formula?
DESEQ
DESEQ2
updated 20 months ago by
ATpoint
★ 4.1k • written 20 months ago by
barrypraveen
• 0
3
votes
2
replies
924
views
DESeq2 is renaming gene names and lack of downregulated genes
DESeq
DESeq2
21 months ago
manwar
• 0
1
vote
1
reply
780
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM
prior
DESeq
LFC
updated 22 months ago by
Michael Love
41k • written 22 months ago by
stew
• 0
1
vote
5
replies
1.2k
views
Error in DEseq
DEseq
RNASeqData
updated 23 months ago by
ATpoint
★ 4.1k • written 23 months ago by
Sanatan
• 0
2
votes
1
reply
1.5k
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 23 months ago by
swbarnes2
★ 1.3k • written 23 months ago by
Hicham
▴ 10
1
vote
5
replies
1.4k
views
Potential outlier/high variance
deseq
DESeq2
updated 2.0 years ago by
Michael Love
41k • written 2.1 years ago by
Amali Thrimawithana
• 0
1
vote
2
replies
914
views
Deseq2 with imbalanced design
Deseq
2.1 years ago
Alex
• 0
1
vote
4
replies
1.6k
views
Test if a gene is NOT differentially expressed in DESeq2?
DESeq2
deseq
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
penny.lane
• 0
0
votes
2
replies
1.1k
views
DESeqDataSet design issue
DESeq
DESeq2
2.4 years ago
matthew.valentine
• 0
19
votes
15
replies
58k
views
DESeq2 output explanation
deseq
deseq2
updated 2.5 years ago by
Michael Love
41k • written 9.5 years ago by
francesca.defilippis
▴ 100
9
votes
6
replies
10k
views
Error bars DESeq or DESeq2 fold change
rnaseq
deseq2
deseq
standard error
confidence interval
updated 2.5 years ago by
Michael Love
41k • written 8.1 years ago by
lisa.crossman
▴ 10
1
vote
1
reply
1.5k
views
DESeq2 rows did not converge in beta, how to solve
DESeq
DESeq2
updated 2.5 years ago by
Michael Love
41k • written 2.5 years ago by
n.vandis
• 0
4
votes
6
replies
1.7k
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r
DESeq
DESeq2
2.6 years ago
s-rhussien
• 0
2
votes
2
replies
2.3k
views
Correct way to make multiple comparisons on DESeq2?
DESeq
DESeq2
R
2.7 years ago • updated 2.6 years ago
jbnrodriguez
▴ 10
1
vote
2
replies
984
views
DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq
DESeq
2.7 years ago
krawczyk.margarita
• 0
0
votes
2
replies
1.5k
views
same padj for all the genes after DEseq analysis
etLRT
WALD
edgeR
DESEq
updated 2.7 years ago by
Michael Love
41k • written 2.7 years ago by
aiswaryabioinfo
• 0
0
votes
1
reply
1.1k
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq
LFC
DEseq
2.9 years ago
ayy2110
• 0
0
votes
7
replies
13k
views
Applying DESeq on RSEM output
edgeR
DESeq
edgeR
DESeq
updated 3.1 years ago by
mehdimerbah
• 0 • written 11.1 years ago by
dvir.tau@gmail.com
▴ 30
1
vote
2
replies
939
views
metage problem with DESeq
DESeq
metagene2
metagene
updated 3.1 years ago by
ericfournier2
▴ 10 • written 3.2 years ago by
GM
▴ 10
10
votes
14
replies
13k
views
how DESeq calculates p-value ?
deseq
differential gene expression
statistics
p-value
updated 3.2 years ago by
Kai_Qi
▴ 20 • written 8.2 years ago by
Giard
▴ 30
0
votes
3
replies
2.2k
views
Understanding MA plot distortion
DESeq2
MAplot
deseq
updated 3.2 years ago by
Michael Love
41k • written 3.2 years ago by
sp
• 0
0
votes
5
replies
1.7k
views
ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2
ZINB
zinbwave
deseq
updated 3.2 years ago by
Michael Love
41k • written 3.2 years ago by
rowcyclecamp
• 0
2
votes
12
replies
4.5k
views
Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2
deseq
updated 3.5 years ago by
Michael Love
41k • written 9.0 years ago by
Nick
• 0
1
vote
2
replies
981
views
DESeq Error (nbinomTest ())
Deseq
nbinomTest
3.9 years ago
canfield
▴ 10
0
votes
7
replies
1.8k
views
DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2
DESeq
nrow == ncol is not TRUE
updated 3.9 years ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
maniermk
• 0
2
votes
2
replies
863
views
Mocking data for understanding interactions in DESeq2
deseq2
deseq
updated 4.1 years ago by
Simon Anders
★ 3.7k • written 4.1 years ago by
blawney
• 0
3
votes
5
replies
2.1k
views
How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq
rna-seq
filtering
DE
deseq2
updated 4.1 years ago by
Michael Love
41k • written 4.1 years ago by
svlachavas
▴ 830
1
vote
9
replies
1.3k
views
Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2
DESeq
updated 4.1 years ago by
Simon Anders
★ 3.7k • written 4.1 years ago by
megapode32559
• 0
0
votes
7
replies
1.1k
views
how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2
deseq
4.3 years ago
MANYA_BIOINFO
• 0
0
votes
1
reply
1.2k
views
DESeq2 counts function not working
deseq2
Deseq
RNAseq
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
mrfossl97
▴ 10
2
votes
3
replies
1.4k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
Keith Hughitt
▴ 180
4
votes
4
replies
4.5k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2
deseq
normalization
updated 4.7 years ago by
wunderl
▴ 40 • written 4.8 years ago by
neekonsu
• 0
1
vote
2
replies
890
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq
deseq2
updated 4.8 years ago by
Michael Love
41k • written 4.8 years ago by
sxv
• 0
0
votes
0
replies
942
views
Including sva results in SeqGSEA with data with batch effect
limma
deseq2
seqgsea
sva
deseq
4.8 years ago
kentfung
▴ 20
0
votes
9
replies
2.0k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq
deseq2
contrast
subgroup
5.2 years ago
ariel
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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