Showing : DEseq • reset
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Can I transform already normalized rna-seq data with Z-score?
Z-score RNASeqData Deseq DESeq2
updated 18 days ago by 63k • written 19 days ago by • 0
0
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3
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271
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Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq DESeq2
updated 8 weeks ago by ★ 3.4k • written 8 weeks ago by ▴ 10
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4
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280
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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 10 weeks ago by 40k • written 11 weeks ago by ▴ 20
1
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2
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329
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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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574
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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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370
views
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
0
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1
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404
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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
1
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1
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350
views
How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 13 months ago by ★ 3.4k • written 13 months ago by • 0
3
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2
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604
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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
533
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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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842
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Error in DEseq
DEseq RNASeqData
updated 16 months ago by ★ 3.4k • written 16 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
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Potential outlier/high variance
deseq DESeq2
updated 17 months ago by 40k • written 18 months ago by • 0
1
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2
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643
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Deseq2 with imbalanced design
Deseq
18 months ago Alex • 0
1
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4
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1.2k
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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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804
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DESeqDataSet design issue
DESeq DESeq2
22 months ago • updated 21 months ago matthew.valentine • 0
1
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1
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1.1k
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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
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
2.0 years ago s-rhussien • 0
2
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2
replies
1.9k
views
Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
2.1 years ago jbnrodriguez ▴ 10
1
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2
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760
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
2.1 years ago krawczyk.margarita • 0
0
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2
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1.1k
views
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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832
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Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
2.4 years ago ayy2110 • 0
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
1
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2
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751
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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
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 2.7 years ago by 40k • written 2.7 years ago by • 0
1
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2
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798
views
DESeq Error (nbinomTest ())
Deseq nbinomTest
3.3 years ago canfield ▴ 10
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7
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1.3k
views
DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2 DESeq nrow == ncol is not TRUE
updated 3.4 years ago by 3.8k • written 3.4 years ago by • 0
2
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5
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4.2k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
written 3.5 years ago by ▴ 10
2
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2
replies
640
views
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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966
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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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873
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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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1.0k
views
DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 3.8 years ago by 40k • written 3.8 years ago by ▴ 10
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3
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1.1k
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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
1
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2
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690
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
4
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4
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3.6k
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TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 4.2 years ago by ▴ 40 • written 4.2 years ago by • 0
0
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0
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753
views
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
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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
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1.6k
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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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825
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
927
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Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
5.0 years ago Ben ▴ 50
0
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7
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3.6k
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DESeq2 install problem
deseq
updated 5.0 years ago by 40k • written 5.0 years ago by • 0
4
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7
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3.0k
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Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 5.0 years ago by 40k • written 5.0 years ago by • 0
0
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3
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854
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DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 5.0 years ago by 40k • written 5.0 years ago by ▴ 60
3
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5
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1.0k
views
Help with multi-factor Deseq analysis
deseq2 rnaseq deseq
updated 5.1 years ago by 40k • written 5.1 years ago by • 0
0
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7
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1.0k
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Deseq 2 multiple comparisons (3 groups, 24 samples)
deseq
updated 5.1 years ago by 40k • written 5.1 years ago by • 0
4
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1
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13k
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The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R deseq tcgabiolinks
5.1 years ago ansari.sarabio • 0
1
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5
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916
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Group Specific Condition Query
deseq2 deseq batcheffect
updated 5.1 years ago by 40k • written 5.1 years ago by ▴ 10
3
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7
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933
views
The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2 deseq
5.2 years ago blastzone.heimerdinger ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Exporting DESeq2 filtered results by James W. MacDonald 63k
I am interested to know what part of my response you found rude. I asked nicely that you don't add to ancient posts, said your post isn't r…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
> I can imagine writing a sparse high-dimensional array in HDF5, but I'm still not sure how to implement the part where it is read and imme…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Not in BioC 3.18. At some point (e.g. in 6 months) they will be deprecated, then 6 months later (i.e. in 1 year) they will be defunct, then…
Comment: Biostrings error at retrieving protein sequences by Hervé Pagès 16k
Yes, but you need to put the clean names back on the AAStringSet object: ``` names(protein_sequences) <- gsub(" .*", "", names(protein_sequ…
Comment: Exporting DESeq2 filtered results by camillab. ▴ 10
thanks! I didn't`t notice that. I will cancel it now!
Votes
Answer: Error MakeOrgPackagefromNCBI
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
A: BiomaRt Arabidopsis genome unavailable
Answer: enrichKEGG
A: Effect of lfcThreshold on p-value in DESeq2
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