Showing : desEQ2 • reset
3
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1.3k
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tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 23 months ago by 68k • written 23 months ago by • 0
0
votes
3
replies
1.3k
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
23 months ago Karthik • 0
0
votes
3
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2.6k
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
23 months ago Oenone • 0
1
vote
1
reply
604
views
Lower FDR cutoff gives more gene counts
DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
1
vote
1
reply
756
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
1
vote
1
reply
722
views
Limma/DESeq2 for unbalanced nested design (paired samples)
limma DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
0
votes
1
reply
797
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How to use DESeq results with LRT vs. with Wald's test
DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
0
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1
reply
839
views
DEseq2 : Complex design with a mixture of male and female mice
statistics DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
0
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2
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1.3k
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio plotPCA DESeq2
23 months ago yee • 0
0
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2
replies
964
views
Batch correction where one of the batches only has a single sample
DESeq2
23 months ago Tom ▴ 10
0
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3
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1.2k
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Deseq2 - Pairwise results from 6 conditions - error non-conformable arguments
DESeq2
23 months ago claire • 0
2
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3
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1.5k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
23 months ago Karthik • 0
0
votes
1
reply
779
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 24 months ago by 43k • written 24 months ago by ▴ 10
2
votes
2
replies
1.1k
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
24 months ago Manthos • 0
1
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4
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1.4k
views
Can DESeq2 be used to compare groups of genes?
DESeq2
24 months ago pl23 • 0
2
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2
replies
1.1k
views
Predicting missing values splines DESeq2
deseq DESeq2
24 months ago georgii.vdovin • 0
0
votes
1
reply
578
views
DESeq2 design with unbalance data and a multifactor design
DESeq2
updated 24 months ago by ★ 5.0k • written 24 months ago by • 0
0
votes
2
replies
1.3k
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
24 months ago anton.kratz ▴ 60
0
votes
1
reply
878
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 24 months ago by ★ 13k • written 2.0 years ago by • 0
4
votes
9
replies
2.1k
views
DESeq2 unable to handle large count values
DESeq2
updated 12 months ago by 43k • written 2.0 years ago by • 0
2
votes
5
replies
2.5k
views
SparseArray unable to install on Bioc 3.18
DESeq2 SummarizedExperiment SparseArray Install DelayedArray
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
0
votes
1
reply
799
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 2.0 years ago by 43k • written 2.1 years ago by • 0
0
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1
reply
888
views
DESeq2: different results with and without releveling when providing contrast
DESeq2
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
0
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1
reply
814
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Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
0
votes
2
replies
956
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
2.0 years ago Ben ▴ 10
0
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9
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3.2k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 2.0 years ago by • 0 • written 8.0 years ago by ▴ 60
0
votes
2
replies
2.6k
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
2.0 years ago RHEA • 0
1
vote
1
reply
601
views
DESeqResults object -> extract statistics results with rownames (gene)
DESeq2
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by ▴ 50
0
votes
7
replies
4.3k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error RStudio ggplot2 DESeq2
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
0
votes
3
replies
875
views
DESeq2: FPMs varying based on sample groups used
DESeq2
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
0
votes
8
replies
1.6k
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
2.0 years ago Luca • 0
0
votes
1
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2.6k
views
Error when trying to create a heatmap with DESeq2
Heatmap RNA-seqanalysis heatmaps DESeq2
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by • 0
2
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10
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2.4k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
2.0 years ago rohitsatyam102 ▴ 20
0
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6
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2.3k
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
2.0 years ago erika.maldonado-rosado • 0
0
votes
2
replies
991
views
How can I devise a method like DESeq2 to give statistics for paired multiple -omic datasets?
DESeq2
updated 2.0 years ago by • 0 • written 2.0 years ago by • 0
0
votes
4
replies
1.4k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 19 months ago by 43k • written 2.0 years ago by • 0
2
votes
3
replies
2.6k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 2.0 years ago by ★ 1.4k • written 2.1 years ago by • 0
0
votes
2
replies
745
views
DESeq2: how could the lower mean abundance treatment show a positive and significant LFC?
DESeq2
2.1 years ago • updated 2.0 years ago Roey Angel • 0
0
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2
replies
1.1k
views
Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
2.1 years ago Karthik • 0
0
votes
1
reply
1.8k
views
DESeq2 Error in Results Contrast and ResultsNames
DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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0
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718
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
2.1 years ago Florian • 0
0
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1
reply
2.2k
views
choosing rank for GSEA
gsea DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
1
vote
1
reply
1.0k
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
votes
3
replies
1.2k
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
1
vote
11
replies
2.9k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
votes
2
replies
1.1k
views
Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
2.1 years ago georgii.vdovin • 0
3
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5
replies
1.7k
views
DESeq2: Design model includes sex but only one female
DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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1
reply
1.7k
views
DeSeq2 normalization 16S
DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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4
replies
1.5k
views
DESeq2 : standardising variation between treatments
RNA-seq DESeq2
2.1 years ago ar14g12 • 0
0
votes
2
replies
843
views
Issues with ddseq2 for treatment response factoring in different KO clones
Clonality RNASeq DESeq2
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by • 0
4,836 results • Page 9 of 97
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Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated by RalphSavage99 • 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Awards • All
Scholar to shepherl 4.2k
Scholar to James W. MacDonald 68k
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Popular Question to edward.esiribloom • 0
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