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Showing :
DESeq
•
reset
1
vote
2
replies
218
views
evaluate the variable importance on genes
DESeq2
deseq
25 days ago
Meme
• 0
0
votes
2
replies
276
views
Running DESeq on normalized data
deseq
DESeq2
updated 3 months ago by
ATpoint
★ 3.9k • written 3 months ago by
Hugo
• 0
2
votes
2
replies
463
views
Predicting missing values splines DESeq2
deseq
DESeq2
4 months ago • updated 3 months ago
georgii.vdovin
• 0
0
votes
1
reply
333
views
Controling for Covariates With a Continuous Predictor Variable
Deseq
DESeq2
updated 4 months ago by
Michael Love
41k • written 4 months ago by
georgii.vdovin
• 0
0
votes
1
reply
572
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
khaserdene99
• 0
0
votes
3
replies
677
views
Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq
DESeq2
updated 7 months ago by
ATpoint
★ 3.9k • written 7 months ago by
Abir.khazaal
▴ 10
0
votes
4
replies
554
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2
apeglm
DESeq
ApeGLM
Ashr
updated 8 months ago by
Michael Love
41k • written 8 months ago by
Ndimensional
▴ 20
1
vote
2
replies
550
views
summarizeToGene in tximeta causing vastly different results
DESeq2
deseq
txime
tximeta
updated 11 months ago by
Michael Love
41k • written 11 months ago by
akrunic
• 0
0
votes
4
replies
1.1k
views
Volcano plot becomes flipped when I add a third condition
DESeq2
volcanoplot
deseq
HELP
contrast
updated 13 months ago by
Basti
▴ 750 • written 13 months ago by
Michael
• 0
0
votes
1
reply
530
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 13 months ago by
Michael Love
41k • written 13 months ago by
m-bihie
▴ 10
0
votes
1
reply
650
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 14 months ago by
Dario Strbenac
★ 1.5k • written 14 months ago by
Hicham
▴ 10
0
votes
2
replies
1.2k
views
suggestions/comments on DESeq transcript wise analysis
convert
DESeq
convert
DESeq
written 12.1 years ago by
Akula, Nirmala NIH/NIMH [C]
▴ 190
1
vote
1
reply
492
views
How to design multifactor DESEQ2 formula?
DESEQ
DESEQ2
updated 18 months ago by
ATpoint
★ 3.9k • written 18 months ago by
barrypraveen
• 0
3
votes
2
replies
872
views
DESeq2 is renaming gene names and lack of downregulated genes
DESeq
DESeq2
20 months ago
manwar
• 0
1
vote
1
reply
738
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM
prior
DESeq
LFC
updated 21 months ago by
Michael Love
41k • written 21 months ago by
stew
• 0
1
vote
5
replies
1.1k
views
Error in DEseq
DEseq
RNASeqData
updated 21 months ago by
ATpoint
★ 3.9k • written 21 months ago by
Sanatan
• 0
2
votes
1
reply
1.4k
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 22 months ago by
swbarnes2
★ 1.3k • written 22 months ago by
Hicham
▴ 10
1
vote
5
replies
1.3k
views
Potential outlier/high variance
deseq
DESeq2
updated 23 months ago by
Michael Love
41k • written 23 months ago by
Amali Thrimawithana
• 0
1
vote
2
replies
848
views
Deseq2 with imbalanced design
Deseq
2.0 years ago
Alex
• 0
1
vote
4
replies
1.4k
views
Test if a gene is NOT differentially expressed in DESeq2?
DESeq2
deseq
updated 2.1 years ago by
Michael Love
41k • written 2.1 years ago by
penny.lane
• 0
0
votes
2
replies
1.0k
views
DESeqDataSet design issue
DESeq
DESeq2
2.3 years ago
matthew.valentine
• 0
1
vote
1
reply
1.4k
views
DESeq2 rows did not converge in beta, how to solve
DESeq
DESeq2
updated 2.4 years ago by
Michael Love
41k • written 2.4 years ago by
n.vandis
• 0
4
votes
6
replies
1.6k
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r
DESeq
DESeq2
2.5 years ago
s-rhussien
• 0
2
votes
2
replies
2.2k
views
Correct way to make multiple comparisons on DESeq2?
DESeq
DESeq2
R
2.5 years ago
jbnrodriguez
▴ 10
1
vote
2
replies
939
views
DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq
DESeq
2.6 years ago
krawczyk.margarita
• 0
0
votes
2
replies
1.4k
views
same padj for all the genes after DEseq analysis
etLRT
WALD
edgeR
DESEq
updated 2.6 years ago by
Michael Love
41k • written 2.6 years ago by
aiswaryabioinfo
• 0
0
votes
1
reply
1.1k
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq
LFC
DEseq
2.8 years ago
ayy2110
• 0
1
vote
2
replies
899
views
metage problem with DESeq
DESeq
metagene2
metagene
updated 3.0 years ago by
ericfournier2
▴ 10 • written 3.0 years ago by
GM
▴ 10
0
votes
3
replies
2.1k
views
Understanding MA plot distortion
DESeq2
MAplot
deseq
updated 3.0 years ago by
Michael Love
41k • written 3.0 years ago by
sp
• 0
0
votes
5
replies
1.6k
views
ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2
ZINB
zinbwave
deseq
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
rowcyclecamp
• 0
2
votes
12
replies
4.3k
views
Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2
deseq
updated 3.4 years ago by
Michael Love
41k • written 8.9 years ago by
Nick
• 0
1
vote
2
replies
948
views
DESeq Error (nbinomTest ())
Deseq
nbinomTest
3.8 years ago
canfield
▴ 10
0
votes
7
replies
1.7k
views
DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2
DESeq
nrow == ncol is not TRUE
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
maniermk
• 0
2
votes
5
replies
5.3k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’
DESeq
written 3.9 years ago by
krunal.24.6
▴ 10
2
votes
2
replies
821
views
Mocking data for understanding interactions in DESeq2
deseq2
deseq
updated 4.0 years ago by
Simon Anders
★ 3.7k • written 4.0 years ago by
blawney
• 0
3
votes
5
replies
2.0k
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 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
svlachavas
▴ 830
1
vote
9
replies
1.2k
views
Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2
DESeq
updated 4.0 years ago by
Simon Anders
★ 3.7k • written 4.0 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
4.1 years ago
MANYA_BIOINFO
• 0
0
votes
1
reply
1.2k
views
DESeq2 counts function not working
deseq2
Deseq
RNAseq
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
mrfossl97
▴ 10
2
votes
3
replies
1.3k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
Keith Hughitt
▴ 180
4
votes
4
replies
4.4k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2
deseq
normalization
updated 4.6 years ago by
wunderl
▴ 40 • written 4.7 years ago by
neekonsu
• 0
1
vote
2
replies
846
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq
deseq2
updated 4.6 years ago by
Michael Love
41k • written 4.6 years ago by
sxv
• 0
0
votes
0
replies
908
views
Including sva results in SeqGSEA with data with batch effect
limma
deseq2
seqgsea
sva
deseq
4.7 years ago
kentfung
▴ 20
0
votes
9
replies
1.9k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq
deseq2
contrast
subgroup
5.1 years ago
ariel
▴ 20
3
votes
12
replies
1.6k
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2
p-value
continuous
deseq
5.1 years ago
ariel
▴ 20
2
votes
3
replies
1.8k
views
DESeq2 count outlier replacement from Cook's threshold
deseq2
deseq
rnaseq
outliers
count outliers
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
lefeverde
▴ 10
0
votes
1
reply
990
views
Question about multi-factor Deseq analysis
DESeq
deseq2
microbiome
gut microbiome
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
FaisalH
• 0
0
votes
3
replies
1.1k
views
Strange lfcShrink plot when running DESeq2 workflow
DESeq2
rnaseq
rna-seq
deseq2
deseq
5.4 years ago
Ben
▴ 50
0
votes
7
replies
3.9k
views
DESeq2 install problem
deseq
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
bikashten
• 0
5
votes
7
replies
3.5k
views
Deseq2 design for one condition over 8 different time point
deseq2
rna-seq
design matrix
deseq
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
thindmarsmission
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: DEG Filtering
by
Amit
• 0
Hello Gordon, The PCA plot for RMA normalized data shows Mixing of samples. Is it Batch Effect ? Because when I apply ARSyNseq() and again …
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
James W. MacDonald
65k
Let's take a closer look. ``` > library(GEOquery) ## some random data > getGEOSuppFiles("GSE193983") > setwd("GSE193983/") > untar("GSE19…
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Votes
Comment: DEG Filtering
Answer: DEG Filtering
Answer: DEG Filtering
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
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