Showing : DEseq • reset
0
votes
1
reply
76
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
8 weeks ago ayy2110 • 0
1
vote
2
replies
188
views
metage problem with DESeq
DESeq metagene2 metagene
updated 4 months ago by ▴ 10 • written 4 months ago by ▴ 10
0
votes
3
replies
249
views
Understanding MA plot distortion
DESeq2 MAplot deseq
updated 4 months ago by 33k • written 4 months ago by • 0
0
votes
5
replies
328
views
ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 5 months ago by 33k • written 5 months ago by • 0
1
vote
12
replies
2.2k
views
Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2 deseq
updated 8 months ago by 33k • written 6.2 years ago by • 0
1
vote
2
replies
187
views
DESeq Error (nbinomTest ())
Deseq nbinomTest
13 months ago canfield ▴ 10
0
votes
7
replies
188
views
DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2 DESeq nrow == ncol is not TRUE
updated 14 months ago by 3.2k • written 14 months ago by • 0
2
votes
3
replies
239
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
updated 15 months ago by 33k • written 15 months ago by ▴ 10
1
vote
2
replies
141
views
Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 15 months ago by ★ 3.7k • written 15 months ago by • 0
3
votes
5
replies
222
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 15 months ago by 33k • written 15 months ago by ▴ 780
1
vote
9
replies
282
views
Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2 DESeq
updated 16 months ago by ★ 3.7k • written 16 months ago by • 0
0
votes
7
replies
278
views
how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
18 months ago husainmanagori1998 • 0
0
votes
1
reply
273
views
DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 19 months ago by 33k • written 19 months ago by • 0
2
votes
3
replies
325
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 20 months ago by 33k • written 20 months ago by ▴ 140
4
votes
4
replies
864
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 23 months ago by ▴ 30 • written 2.0 years ago by • 0
1
vote
2
replies
275
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 24 months ago by 33k • written 24 months ago by • 0
0
votes
0
replies
291
views
Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
2.0 years ago kentfung • 0
0
votes
9
replies
541
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
2.4 years ago ariel • 0
3
votes
12
replies
442
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
2.4 years ago ariel • 0
2
votes
3
replies
735
views
DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 2.6 years ago by 33k • written 2.6 years ago by ▴ 10
0
votes
1
reply
343
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 2.7 years ago by 33k • written 2.7 years ago by • 0
0
votes
3
replies
461
views
Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
2.8 years ago Ben ▴ 20
0
votes
7
replies
2.0k
views
DESeq2 install problem
deseq
updated 2.8 years ago by 33k • written 2.8 years ago by • 0
4
votes
7
replies
1.4k
views
Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 2.8 years ago by 33k • written 2.8 years ago by • 0
0
votes
3
replies
426
views
DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 2.8 years ago by 33k • written 2.8 years ago by ▴ 60
3
votes
5
replies
523
views
Help with multi-factor Deseq analysis
deseq2 rnaseq deseq
updated 2.9 years ago by 33k • written 2.9 years ago by • 0
0
votes
7
replies
499
views
Deseq 2 multiple comparisons (3 groups, 24 samples)
deseq
updated 2.9 years ago by 33k • written 2.9 years ago by • 0
4
votes
1
reply
12k
views
The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R deseq tcgabiolinks
2.9 years ago ansari.sarabio • 0
1
vote
5
replies
421
views
Group Specific Condition Query
deseq2 deseq batcheffect
updated 2.9 years ago by 33k • written 2.9 years ago by • 0
3
votes
7
replies
474
views
The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2 deseq
3.0 years ago blastzone.heimerdinger • 0
0
votes
8
replies
736
views
DESeq2 Multi factor, multi time point comparison design formula
rna-seq deseq2 deseq R
updated 3.0 years ago by 33k • written 3.0 years ago by • 0
0
votes
1
reply
340
views
how to start normalization
deseq
3.0 years ago raghavaraghava049 • 0
0
votes
1
reply
351
views
Basemean always multiples of 0.5 in deseq2 results
deseq results baseMean
updated 3.0 years ago by 33k • written 3.0 years ago by • 0
0
votes
3
replies
376
views
3x2 comparisons in DEseq - time (3 time points) and two treatments
deseq2 deseq rna-seq multiple comparisons
updated 3.1 years ago by 33k • written 3.1 years ago by ▴ 60
2
votes
3
replies
682
views
ASE using DESeq2
deseq2 deseq normalization allele specific expression rnaseq
updated 3.1 years ago by ★ 3.7k • written 3.1 years ago by • 0
0
votes
5
replies
550
views
How to simulate time course RNA seq data using DESeq?
deseq2 R makeexampledeseqdataset deseq
updated 3.2 years ago by 33k • written 3.2 years ago by • 0
3
votes
7
replies
961
views
novice: building gene co-expression network using RNA-Seq data
rna-seq WGCNA deseq method coexpression
updated 3.3 years ago by ★ 2.6k • written 3.3 years ago by ▴ 10
1
vote
2
replies
574
views
Deseq2 with replicate mean and variance information
deseq2 deseq differential analysis proteomics
3.3 years ago blehtine • 0
1
vote
8
replies
1.2k
views
DESeq2 : group specific effect of a treatment while controlling for individual effect
deseq2 DESeq design and contrast matrix deseq
3.4 years ago • updated 3.3 years ago SPbeginner • 0
1
vote
3
replies
553
views
DEseq2 sample imbalance
deseq
3.4 years ago • updated 3.3 years ago aishu.jp ▴ 20
0
votes
4
replies
12k
views
Normalization by DEseq
Genetics Normalization DESeq Genetics Normalization DESeq
updated 3.4 years ago by • 0 • written 10.8 years ago by ▴ 20
0
votes
8
replies
1.5k
views
Comparing between two differential expression analysis - two different fold changes
Deseq deseq2 differential gene expression rnaseq statistical test
3.4 years ago Marina • 0
0
votes
4
replies
569
views
Normalise counts when tumour samples have normal tissue contamination.
deseq2 deseq edgeR rnaseq htseqcounts
3.4 years ago Deepali • 0
0
votes
2
replies
1.9k
views
Problem loading or running DESeq2
deseq could not find function
updated 3.4 years ago by 33k • written 3.4 years ago by • 0
5
votes
3
replies
2.2k
views
DESeq2 with interaction using SVA
deseq2 sva interaction term grouping variable deseq
3.5 years ago kevin.kingsland ▴ 40
4
votes
6
replies
654
views
DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 3.5 years ago by 33k • written 3.5 years ago by ▴ 60
2
votes
10
replies
1.1k
views
DESeq2 results export padj sorted
deseq2 deseq differential binding analysis
updated 3.5 years ago by 33k • written 3.5 years ago by ▴ 60
2
votes
4
replies
767
views
Matrix not full rank - DESeq2
deseq2 model matrix not full rank model.matrix deseq differential binding analysis
updated 3.5 years ago by ★ 3.7k • written 3.5 years ago by ▴ 60
2
votes
5
replies
603
views
Mapping DESeq2 output back to chromosomal positions
deseq2 deseq diffbind differential binding analysis
updated 3.6 years ago by 33k • written 3.6 years ago by ▴ 60
40
votes
44
replies
5.9k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 3.6 years ago by ▴ 60 • written 4.2 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: edgeR by Gitanjali • 0
Thanks @gordonsmyth , that helped. Also how do I put 24h at the end? I want to plot the observed and fitted values for each gene across tim…
Comment: ChIPseeker genomicAnnotationPriority by hqlkjx • 0
I am meeting the same problem
Comment: cannot install edgeR on M1 Mac by Gordon Smyth 43k
OK, I understand now the issue is that you are running R compiled for the Mac M1 ARM-based processor but Bioconductor doesn't provide binar…
Comment: How can I use geom_label_repel with EnhancedVolcano? by Kevin Blighe 3.2k
Thanks! I think that I know what you want to do, but, unfortunately, that level of customisation is not possible with *EnhancedVolcano* alo…
Comment: Split mzID file with mzID() function by Brem • 0
Thank you, I've edited the post with the correct package, mzID.
Votes
ChIPseeker genomicAnnotationPriority
Answer: barcodeRanks unusual warning "In smooth.spline(x[new.keep], y[new.keep], df = df
Answer: barcodeRanks unusual warning "In smooth.spline(x[new.keep], y[new.keep], df = df
cannot install edgeR on M1 Mac
Increasing rlm iterations for convergence in limma's normalizeRobustSpline
Awards • All
Scholar to Aaron Lun ★ 27k
Popular Question to Michael Love 33k
Popular Question to Gordon Smyth 43k
Prophet to shepherl 2.8k
Teacher to Rory Stark ★ 4.0k
Locations • All
India, 28 minutes ago
Rockefeller University, New York City, 38 minutes ago
The city by the bay, 49 minutes ago
Netherlands, 1 hour ago
University of Salerno, Salerno, Italy, 1 hour ago
Traffic: 340 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