Showing : Deseq • reset
1
vote
2
replies
289
views
evaluate the variable importance on genes
DESeq2 deseq
8 weeks ago Meme • 0
0
votes
2
replies
318
views
Running DESeq on normalized data
deseq DESeq2
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
2
votes
2
replies
501
views
Predicting missing values splines DESeq2
deseq DESeq2
5 months ago georgii.vdovin • 0
0
votes
1
reply
363
views
Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 5 months ago by 41k • written 5 months ago by • 0
0
votes
1
reply
625
views
Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 7 months ago by 65k • written 7 months ago by • 0
0
votes
3
replies
837
views
Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq DESeq2
updated 8 months ago by ★ 4.0k • written 8 months ago by ▴ 10
0
votes
4
replies
618
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 41k • written 9 months ago by ▴ 20
1
vote
2
replies
600
views
summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 12 months ago by 41k • written 12 months ago by • 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 ▴ 770 • written 14 months ago by • 0
0
votes
1
reply
553
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 14 months ago by 41k • written 14 months ago by ▴ 10
0
votes
1
reply
701
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 ★ 1.5k • written 15 months ago by ▴ 10
1
vote
1
reply
513
views
How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 19 months ago by ★ 4.0k • written 19 months ago by • 0
3
votes
2
replies
905
views
DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
21 months ago manwar • 0
1
vote
1
reply
765
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 22 months ago by 41k • written 22 months ago by • 0
1
vote
5
replies
1.2k
views
Error in DEseq
DEseq RNASeqData
updated 22 months ago by ★ 4.0k • written 22 months ago by • 0
2
votes
1
reply
1.4k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 23 months ago by ★ 1.3k • written 23 months ago by ▴ 10
1
vote
5
replies
1.4k
views
Potential outlier/high variance
deseq DESeq2
updated 24 months ago by 41k • written 2.0 years ago by • 0
1
vote
2
replies
894
views
Deseq2 with imbalanced design
Deseq
2.1 years ago Alex • 0
1
vote
4
replies
1.5k
views
Test if a gene is NOT differentially expressed in DESeq2?
DESeq2 deseq
updated 2.2 years ago by 41k • written 2.2 years ago by • 0
0
votes
2
replies
1.0k
views
DESeqDataSet design issue
DESeq DESeq2
2.4 years ago • updated 2.3 years ago matthew.valentine • 0
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 41k • written 2.5 years ago by • 0
4
votes
6
replies
1.6k
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
2.2k
views
Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
2.6 years ago jbnrodriguez ▴ 10
1
vote
2
replies
967
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
1.5k
views
same padj for all the genes after DEseq analysis
etLRT WALD edgeR DESEq
updated 2.7 years ago by 41k • written 2.7 years ago by • 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
3
replies
2.2k
views
Understanding MA plot distortion
DESeq2 MAplot deseq
updated 3.1 years ago by 41k • written 3.1 years ago by • 0
1
vote
2
replies
928
views
metage problem with DESeq
DESeq metagene2 metagene
updated 3.1 years ago by ▴ 10 • written 3.1 years ago by ▴ 10
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 41k • written 3.2 years ago by • 0
1
vote
2
replies
972
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 ★ 3.9k • written 3.9 years ago by • 0
2
votes
5
replies
5.5k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
written 4.0 years ago by ▴ 10
2
votes
2
replies
846
views
Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 4.0 years ago by ★ 3.7k • written 4.0 years ago by • 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 4.0 years ago by 41k • written 4.0 years ago by ▴ 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 ★ 3.7k • written 4.1 years ago by • 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
4.2 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 41k • written 4.4 years ago by ▴ 10
2
votes
3
replies
1.4k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 4.4 years ago by 41k • written 4.4 years ago by ▴ 180
1
vote
2
replies
877
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 4.7 years ago by 41k • written 4.7 years ago by • 0
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 ▴ 40 • written 4.7 years ago by • 0
0
votes
0
replies
932
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
3
votes
12
replies
1.6k
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
5.2 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 5.4 years ago by 41k • written 5.4 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
0
votes
3
replies
1.2k
views
Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
5.5 years ago Ben ▴ 50
0
votes
7
replies
3.9k
views
DESeq2 install problem
deseq
updated 5.5 years ago by 41k • written 5.5 years ago by • 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 41k • written 5.5 years ago by ▴ 10
0
votes
3
replies
1.0k
views
DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 5.6 years ago by 41k • written 5.6 years ago by ▴ 60
3
votes
5
replies
1.3k
views
Help with multi-factor Deseq analysis
deseq2 rnaseq deseq
updated 5.6 years ago by 41k • written 5.6 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Awards • All
Popular Question to shepherl 3.8k
Popular Question to BioinfGuru ▴ 30
Popular Question to Gordon Smyth 50k
Scholar to Peter Hickey ▴ 740
Popular Question to sropri • 0
Locations • All
United States, 2 minutes ago
United States, 4 minutes ago
United States, 7 minutes ago
United States, 11 minutes ago
France, 13 minutes ago
Traffic: 885 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6