Showing : Deseq • reset
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evaluate the variable importance on genes
DESeq2 deseq
8 weeks ago Meme • 0
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2
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327
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Running DESeq on normalized data
deseq DESeq2
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
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506
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Predicting missing values splines DESeq2
deseq DESeq2
5 months ago georgii.vdovin • 0
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369
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Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 5 months ago by 41k • written 5 months ago by • 0
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639
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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
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3
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865
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Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq DESeq2
updated 8 months ago by ★ 4.0k • written 8 months ago by ▴ 10
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11
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With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq deseq2
updated 8 months ago by • 0 • written 9.2 years ago by ▴ 40
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4
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629
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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
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5
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5.6k
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ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
written 4.0 years ago by ▴ 10
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604
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summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 12 months ago by 41k • written 12 months ago by • 0
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4
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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
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1
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559
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What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 15 months ago by 41k • written 15 months ago by ▴ 10
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1
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711
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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
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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
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2
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1.2k
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suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 12.2 years ago by ▴ 190
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1
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517
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How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 19 months ago by ★ 4.0k • written 19 months ago by • 0
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2
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913
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DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
21 months ago manwar • 0
1
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1
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772
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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
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5
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1.2k
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Error in DEseq
DEseq RNASeqData
updated 22 months ago by ★ 4.0k • written 22 months ago by • 0
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1
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1.5k
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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
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5
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1.4k
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Potential outlier/high variance
deseq DESeq2
updated 24 months ago by 41k • written 2.0 years ago by • 0
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899
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Deseq2 with imbalanced design
Deseq
2.1 years ago Alex • 0
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4
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1.5k
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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
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1.1k
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DESeqDataSet design issue
DESeq DESeq2
2.4 years ago matthew.valentine • 0
19
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15
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58k
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DESeq2 output explanation
deseq deseq2
updated 2.5 years ago by 41k • written 9.5 years ago by ▴ 100
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10k
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Error bars DESeq or DESeq2 fold change
rnaseq deseq2 deseq standard error confidence interval
updated 2.5 years ago by 41k • written 8.0 years ago by ▴ 10
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1
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1.5k
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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
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1.7k
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Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
2.6 years ago s-rhussien • 0
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
2.6 years ago jbnrodriguez ▴ 10
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
2.7 years ago krawczyk.margarita • 0
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1.5k
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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
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
2.9 years ago ayy2110 • 0
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Applying DESeq on RSEM output
edgeR DESeq edgeR DESeq
updated 3.1 years ago by • 0 • written 11.1 years ago by ▴ 30
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931
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metage problem with DESeq
DESeq metagene2 metagene
updated 3.1 years ago by ▴ 10 • written 3.1 years ago by ▴ 10
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14
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13k
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how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 3.1 years ago by ▴ 20 • written 8.2 years ago by ▴ 30
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3
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2.2k
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Understanding MA plot distortion
DESeq2 MAplot deseq
updated 3.1 years ago by 41k • written 3.1 years ago by • 0
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1.7k
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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
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12
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Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2 deseq
updated 3.5 years ago by 41k • written 9.0 years ago by • 0
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DESeq Error (nbinomTest ())
Deseq nbinomTest
3.9 years ago canfield ▴ 10
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1.8k
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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
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2
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855
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Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 4.1 years ago by ★ 3.7k • written 4.1 years ago by • 0
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5
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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 41k • written 4.1 years ago by ▴ 830
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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
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how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
4.2 years ago MANYA_BIOINFO • 0
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1
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1.2k
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DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 4.4 years ago by 41k • written 4.4 years ago by ▴ 10
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3
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1.4k
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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
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4
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4.5k
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TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 4.7 years ago by ▴ 40 • written 4.8 years ago by • 0
1
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882
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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
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935
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Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
4.8 years ago kentfung ▴ 20
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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: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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Scholar to James W. MacDonald 65k
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