Showing : Deseq • reset
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evaluate the variable importance on genes
DESeq2 deseq
8 weeks ago • updated 7 weeks ago Meme • 0
0
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2
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318
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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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2
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500
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Predicting missing values splines DESeq2
deseq DESeq2
5 months ago georgii.vdovin • 0
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1
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363
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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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1
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624
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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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829
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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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26k
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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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616
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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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5.5k
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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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2
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598
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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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1.2k
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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
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1
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553
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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
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1
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701
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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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2.8k
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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 15 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
1
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1
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513
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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
3
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2
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905
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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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763
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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
1
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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
2
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1
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1.4k
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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
1
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2
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894
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Deseq2 with imbalanced design
Deseq
2.1 years ago Alex • 0
1
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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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2
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1.0k
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DESeqDataSet design issue
DESeq DESeq2
2.3 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 2.4 years ago by 41k • written 9.4 years ago by ▴ 100
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6
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10k
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Error bars DESeq or DESeq2 fold change
rnaseq deseq2 deseq standard error confidence interval
updated 2.4 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
4
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6
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1.6k
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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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2
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2.2k
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
2.6 years ago jbnrodriguez ▴ 10
1
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2
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967
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
2.6 years ago krawczyk.margarita • 0
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2
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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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1
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1.1k
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
2.9 years ago ayy2110 • 0
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7
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13k
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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
1
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2
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928
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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
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
0
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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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5
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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
2
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12
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4.4k
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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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971
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DESeq Error (nbinomTest ())
Deseq nbinomTest
3.9 years ago canfield ▴ 10
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7
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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
2
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2
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845
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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
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5
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2.1k
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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 4.0 years ago by 41k • written 4.0 years ago by ▴ 830
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9
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1.3k
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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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7
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1.1k
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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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4.4k
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TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 4.7 years ago by ▴ 40 • written 4.7 years ago by • 0
1
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2
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877
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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
0
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0
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931
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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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9
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2.0k
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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 ...
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Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Votes
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
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Awards • All
Scholar to Peter Hickey ▴ 740
Popular Question to sropri • 0
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