Showing : DESEq • reset
1
vote
2
replies
322
views
evaluate the variable importance on genes
DESeq2 deseq
10 weeks ago Meme • 0
0
votes
2
replies
342
views
Running DESeq on normalized data
deseq DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
2
votes
2
replies
526
views
Predicting missing values splines DESeq2
deseq DESeq2
5 months ago georgii.vdovin • 0
0
votes
1
reply
385
views
Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 6 months ago by 42k • written 6 months ago by • 0
0
votes
1
reply
658
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
907
views
Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq DESeq2
updated 9 months ago by ★ 4.1k • written 9 months ago by ▴ 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 • 0 • written 9.3 years ago by ▴ 40
0
votes
4
replies
663
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 42k • written 9 months ago by ▴ 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 ▴ 10
1
vote
2
replies
618
views
summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 12 months ago by 42k • written 12 months ago by • 0
0
votes
4
replies
1.3k
views
Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 14 months ago by ▴ 780 • written 14 months ago by • 0
0
votes
1
reply
568
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 15 months ago by 42k • written 15 months ago by ▴ 10
0
votes
1
reply
734
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
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 50k • written 11.9 years ago by ★ 6.5k
0
votes
2
replies
1.3k
views
suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 12.2 years ago by ▴ 190
1
vote
1
reply
523
views
How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 20 months ago by ★ 4.1k • written 20 months ago by • 0
3
votes
2
replies
934
views
DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
21 months ago manwar • 0
1
vote
1
reply
784
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 23 months ago by 42k • written 23 months ago by • 0
1
vote
5
replies
1.2k
views
Error in DEseq
DEseq RNASeqData
updated 23 months ago by ★ 4.1k • written 23 months ago by • 0
2
votes
1
reply
1.5k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 24 months ago by ★ 1.3k • written 24 months ago by ▴ 10
1
vote
5
replies
1.4k
views
Potential outlier/high variance
deseq DESeq2
updated 2.0 years ago by 42k • written 2.1 years ago by • 0
1
vote
2
replies
920
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 42k • written 2.3 years ago by • 0
0
votes
2
replies
1.1k
views
DESeqDataSet design issue
DESeq DESeq2
2.4 years ago matthew.valentine • 0
19
votes
15
replies
59k
views
DESeq2 output explanation
deseq deseq2
updated 2.5 years ago by 42k • written 9.5 years ago by ▴ 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 42k • written 8.1 years ago by ▴ 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 42k • written 2.5 years ago by • 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
987
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 42k • 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
7
replies
13k
views
Applying DESeq on RSEM output
edgeR DESeq edgeR DESeq
updated 3.1 years ago by • 0 • written 11.1 years ago by ▴ 30
1
vote
2
replies
945
views
metage problem with DESeq
DESeq metagene2 metagene
updated 3.1 years ago by ▴ 10 • written 3.2 years ago by ▴ 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 ▴ 20 • written 8.2 years ago by ▴ 30
0
votes
3
replies
2.3k
views
Understanding MA plot distortion
DESeq2 MAplot deseq
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
0
votes
5
replies
1.8k
views
ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 3.3 years ago by 42k • written 3.3 years ago by • 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 42k • written 9.0 years ago by • 0
1
vote
2
replies
983
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
2
replies
867
views
Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 4.1 years ago by ★ 3.7k • written 4.1 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 4.1 years ago by 42k • written 4.1 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
1.2k
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
1.3k
views
DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 4.4 years ago by 42k • 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 4.5 years ago by 42k • written 4.5 years ago by ▴ 180
4
votes
4
replies
4.5k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 4.8 years ago by ▴ 40 • written 4.8 years ago by • 0
1
vote
2
replies
895
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 4.8 years ago by 42k • written 4.8 years ago by • 0
0
votes
0
replies
947
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: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and gives inflated significance, as we showed in our 2012 pap…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Awards • All
Popular Question to Gyan Prakash Mishra ▴ 10
Popular Question to Gordon Smyth 50k
Popular Question to WouterDeCoster ▴ 130
Scholar to Michael Love 42k
Popular Question to Malcolm Cook ★ 1.6k
Locations • All
UPF, Barcelona, Spain, 2 minutes ago
Melbourne, Australia, 4 minutes ago
INDIA, 7 minutes ago
WEHI, Melbourne, Australia, 16 minutes ago
United States, 27 minutes ago
Traffic: 660 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