Showing : DEseq • reset
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Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 10 days ago by 63k • written 10 days ago by • 0
0
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3
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260
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Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq DESeq2
updated 7 weeks ago by ★ 3.4k • written 7 weeks ago by ▴ 10
5
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11
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25k
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With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq deseq2
updated 7 weeks ago by • 0 • written 8.7 years ago by ▴ 30
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4
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274
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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 weeks ago by 40k • written 10 weeks ago by ▴ 20
2
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5
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4.2k
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ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
written 3.4 years ago by ▴ 10
1
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2
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322
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summarizeToGene in tximeta causing vastly different results
DESeq2 deseq txime tximeta
updated 5 months ago by 40k • written 5 months ago by • 0
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4
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564
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Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 7 months ago by ▴ 720 • written 7 months ago by • 0
0
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1
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367
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What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 8 months ago by 40k • written 8 months ago by ▴ 10
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1
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396
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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 8 months ago by ★ 1.5k • written 8 months ago by ▴ 10
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1
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2.6k
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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 8 months ago by 48k • written 11.3 years ago by 6.5k
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2
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1.0k
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suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 11.6 years ago by ▴ 190
1
vote
1
reply
348
views
How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 12 months ago by ★ 3.4k • written 12 months ago by • 0
3
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2
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592
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DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
14 months ago manwar • 0
1
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1
reply
523
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 15 months ago by 40k • written 15 months ago by • 0
1
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5
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824
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Error in DEseq
DEseq RNASeqData
updated 15 months ago by ★ 3.4k • written 15 months ago by • 0
2
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1
reply
1.1k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 16 months ago by ★ 1.3k • written 16 months ago by ▴ 10
1
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5
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1.0k
views
Potential outlier/high variance
deseq DESeq2
updated 17 months ago by 40k • written 17 months ago by • 0
1
vote
2
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634
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Deseq2 with imbalanced design
Deseq
18 months ago Alex • 0
1
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4
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1.1k
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Test if a gene is NOT differentially expressed in DESeq2?
DESeq2 deseq
updated 20 months ago by 40k • written 20 months ago by • 0
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2
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793
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DESeqDataSet design issue
DESeq DESeq2
21 months ago matthew.valentine • 0
17
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15
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53k
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DESeq2 output explanation
deseq deseq2
updated 22 months ago by 40k • written 8.9 years ago by ▴ 100
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6
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8.9k
views
Error bars DESeq or DESeq2 fold change
rnaseq deseq2 deseq standard error confidence interval
updated 22 months ago by 40k • written 7.5 years ago by ▴ 10
1
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1
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1.1k
views
DESeq2 rows did not converge in beta, how to solve
DESeq DESeq2
updated 23 months ago by 40k • written 23 months ago by • 0
4
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6
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1.3k
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Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
24 months ago s-rhussien • 0
2
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2
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1.8k
views
Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
2.1 years ago • updated 2.0 years ago jbnrodriguez ▴ 10
1
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2
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752
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
2.1 years ago krawczyk.margarita • 0
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2
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1.1k
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same padj for all the genes after DEseq analysis
etLRT WALD edgeR DESEq
updated 2.1 years ago by 40k • written 2.1 years ago by • 0
0
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1
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816
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
2.3 years ago ayy2110 • 0
0
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7
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12k
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Applying DESeq on RSEM output
edgeR DESeq edgeR DESeq
updated 2.5 years ago by • 0 • written 10.5 years ago by ▴ 30
1
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2
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739
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metage problem with DESeq
DESeq metagene2 metagene
updated 2.5 years ago by ▴ 10 • written 2.6 years ago by ▴ 10
10
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14
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11k
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how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 2.6 years ago by ▴ 20 • written 7.6 years ago by ▴ 30
0
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3
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1.6k
views
Understanding MA plot distortion
DESeq2 MAplot deseq
updated 2.6 years ago by 40k • written 2.6 years ago by • 0
0
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5
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1.3k
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ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 2.6 years ago by 40k • written 2.6 years ago by • 0
2
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12
replies
3.8k
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Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2 deseq
updated 2.9 years ago by 40k • written 8.4 years ago by • 0
1
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2
replies
790
views
DESeq Error (nbinomTest ())
Deseq nbinomTest
3.3 years ago canfield ▴ 10
0
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7
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1.3k
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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 3.3 years ago by 3.8k • written 3.3 years ago by • 0
2
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2
replies
626
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Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 3.5 years ago by ★ 3.7k • written 3.5 years ago by • 0
3
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5
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1.6k
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 3.5 years ago by 40k • written 3.5 years ago by ▴ 810
1
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9
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948
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Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2 DESeq
updated 3.5 years ago by ★ 3.7k • written 3.5 years ago by • 0
0
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7
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857
views
how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
3.7 years ago MANYA_BIOINFO • 0
0
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1
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992
views
DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 3.8 years ago by 40k • written 3.8 years ago by ▴ 10
2
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3
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1.1k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 3.9 years ago by 40k • written 3.9 years ago by ▴ 180
4
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4
replies
3.6k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 4.1 years ago by ▴ 40 • written 4.2 years ago by • 0
1
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2
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679
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 4.2 years ago by 40k • written 4.2 years ago by • 0
0
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0
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748
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Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
4.2 years ago kentfung ▴ 10
0
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9
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1.5k
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NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
4.6 years ago ariel ▴ 10
3
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12
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1.2k
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
4.6 years ago ariel ▴ 10
2
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3
replies
1.6k
views
DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 4.8 years ago by 40k • written 4.8 years ago by ▴ 10
0
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1
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822
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 4.9 years ago by 40k • written 4.9 years ago by • 0
0
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3
replies
921
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Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
5.0 years ago Ben ▴ 50
50 results • Page 1 of 1
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Comment: LIMMA dupcor() function time issue. by Gordon Smyth 48k
That's ok, but there is nothing to be gained by subsetting 1000 times. It would be better to simply subset 100,000 rows once, although the …
Comment: Specifying evidence channels in STRINGdb by robynne.braun • 0
Also I found prior thread here addressing the same question with response that functionality will be supported someday. This was a few year…
Comment: Problems with FLOWAI by SHASHI • 0
please try this using short path name and keeping your fcs file and wsp file in your local directory https://youtu.be/xLeqE7PNYzA
Comment: DataFrame Construction With Non-standard Column by Hervé Pagès 16k
SimpleList is a List derivative and List derivatives in general don't need protection. For example, a GRangesList object (which is also a L…
Answer: Deseq2, how to model design for comparing Mutant mouse at age 14 days versus Mu by swbarnes2 ★ 1.3k
The Status grouping you show above is good to use if you want to simply compare one subset of samples to another subset. The ~Genotype +…
Votes
Answer: Deseq2, enrichGO and ensembl ID
A: LIMMA dupcor() function time issue.
A: LIMMA dupcor() function time issue.
Answer: Further analysis after limma regression output
A: collapseReplicates in DESeq2
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