Showing : DEseq • reset
0
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2
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150
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DESeqDataSet design issue
DESeq DESeq2
5 weeks ago matthew.valentine • 0
1
vote
1
reply
164
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DESeq2 rows did not converge in beta, how to solve
DESeq DESeq2
updated 12 weeks ago by 35k • written 12 weeks ago by • 0
4
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6
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394
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Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
3 months ago s-rhussien • 0
1
vote
2
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313
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
4 months ago jbnrodriguez • 0
1
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2
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218
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
4 months ago krawczyk.margarita • 0
0
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2
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256
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same padj for all the genes after DEseq analysis
etLRT WALD edgeR DESEq
updated 5 months ago by 35k • written 5 months ago by • 0
0
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1
reply
177
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
8 months ago ayy2110 • 0
1
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2
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307
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metage problem with DESeq
DESeq metagene2 metagene
updated 10 months ago by ▴ 10 • written 10 months ago by ▴ 10
0
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3
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448
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Understanding MA plot distortion
DESeq2 MAplot deseq
updated 10 months ago by 35k • written 10 months ago by • 0
0
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5
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524
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ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 11 months ago by 35k • written 11 months ago by • 0
1
vote
12
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2.5k
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Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2 deseq
updated 14 months ago by 35k • written 6.7 years ago by • 0
1
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2
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381
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DESeq Error (nbinomTest ())
Deseq nbinomTest
19 months ago canfield ▴ 10
0
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7
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321
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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 20 months ago by 3.4k • written 20 months ago by • 0
2
votes
3
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584
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ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’ DESeq
updated 21 months ago by 35k • written 21 months ago by ▴ 10
1
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2
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232
views
Mocking data for understanding interactions in DESeq2
deseq2 deseq
updated 21 months ago by ★ 3.7k • written 21 months ago by • 0
3
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5
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397
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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 22 months ago by 35k • written 22 months ago by ▴ 780
1
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9
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442
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Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2 DESeq
updated 22 months ago by ★ 3.7k • written 22 months ago by • 0
0
votes
7
replies
414
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how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
24 months ago husainmanagori1998 • 0
0
votes
1
reply
417
views
DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 2.1 years ago by 35k • written 2.1 years ago by ▴ 10
2
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3
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504
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 2.2 years ago by 35k • written 2.2 years ago by ▴ 150
4
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4
replies
1.3k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2 deseq normalization
updated 2.5 years ago by ▴ 30 • written 2.5 years ago by • 0
1
vote
2
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373
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 2.5 years ago by 35k • written 2.5 years ago by • 0
0
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0
replies
421
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Including sva results in SeqGSEA with data with batch effect
limma deseq2 seqgsea sva deseq
2.5 years ago kentfung • 0
0
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9
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734
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NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
2.9 years ago ariel ▴ 10
3
votes
12
replies
677
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Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
2.9 years ago ariel ▴ 10
2
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3
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921
views
DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 3.1 years ago by 35k • written 3.1 years ago by ▴ 10
0
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1
reply
436
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 3.2 years ago by 35k • written 3.2 years ago by • 0
0
votes
3
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564
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Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
3.3 years ago Ben ▴ 30
0
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7
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2.2k
views
DESeq2 install problem
deseq
updated 3.3 years ago by 35k • written 3.3 years ago by • 0
4
votes
7
replies
1.8k
views
Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 3.3 years ago by 35k • written 3.3 years ago by • 0
0
votes
3
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515
views
DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 3.3 years ago by 35k • written 3.3 years ago by ▴ 60
3
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5
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603
views
Help with multi-factor Deseq analysis
deseq2 rnaseq deseq
updated 3.4 years ago by 35k • written 3.4 years ago by • 0
0
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7
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632
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Deseq 2 multiple comparisons (3 groups, 24 samples)
deseq
updated 3.4 years ago by 35k • written 3.4 years ago by • 0
4
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1
reply
12k
views
The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R deseq tcgabiolinks
3.4 years ago ansari.sarabio • 0
1
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5
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511
views
Group Specific Condition Query
deseq2 deseq batcheffect
updated 3.4 years ago by 35k • written 3.4 years ago by • 0
3
votes
7
replies
562
views
The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2 deseq
3.5 years ago blastzone.heimerdinger ▴ 10
0
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8
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980
views
DESeq2 Multi factor, multi time point comparison design formula
rna-seq deseq2 deseq R
updated 3.5 years ago by 35k • written 3.5 years ago by • 0
0
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1
reply
410
views
how to start normalization
deseq
3.5 years ago raghavaraghava049 • 0
0
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1
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447
views
Basemean always multiples of 0.5 in deseq2 results
deseq results baseMean
updated 3.5 years ago by 35k • written 3.5 years ago by • 0
0
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3
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452
views
3x2 comparisons in DEseq - time (3 time points) and two treatments
deseq2 deseq rna-seq multiple comparisons
updated 3.6 years ago by 35k • written 3.6 years ago by ▴ 60
2
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3
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787
views
ASE using DESeq2
deseq2 deseq normalization allele specific expression rnaseq
updated 3.6 years ago by ★ 3.7k • written 3.6 years ago by • 0
0
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5
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653
views
How to simulate time course RNA seq data using DESeq?
deseq2 R makeexampledeseqdataset deseq
updated 3.7 years ago by 35k • written 3.7 years ago by • 0
3
votes
7
replies
1.2k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq WGCNA deseq method coexpression
updated 3.8 years ago by ★ 2.6k • written 3.8 years ago by ▴ 10
1
vote
2
replies
773
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Deseq2 with replicate mean and variance information
deseq2 deseq differential analysis proteomics
3.8 years ago blehtine • 0
1
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8
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1.4k
views
DESeq2 : group specific effect of a treatment while controlling for individual effect
deseq2 DESeq design and contrast matrix deseq
3.9 years ago • updated 3.8 years ago SPbeginner • 0
1
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3
replies
668
views
DEseq2 sample imbalance
deseq
3.9 years ago • updated 3.8 years ago aishu.jp ▴ 20
0
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4
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12k
views
Normalization by DEseq
Genetics Normalization DESeq Genetics Normalization DESeq
updated 3.9 years ago by • 0 • written 11.3 years ago by ▴ 20
0
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8
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1.9k
views
Comparing between two differential expression analysis - two different fold changes
Deseq deseq2 differential gene expression rnaseq statistical test
3.9 years ago Marina • 0
0
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4
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696
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Normalise counts when tumour samples have normal tissue contamination.
deseq2 deseq edgeR rnaseq htseqcounts
3.9 years ago Deepali • 0
0
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2
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2.4k
views
Problem loading or running DESeq2
deseq could not find function
updated 3.9 years ago by 35k • written 3.9 years ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: DiffBind dba.count Error in if (sum(tokeep) < length(tokeep)) by tjhwangxiong • 0
``` https://drive.google.com/drive/folders/1787thVatZpt_KFrfXY-aXV1m0FRm8Mhm?usp=sharing ``` Thanks for your reply. I have uploaded the fil…
Comment: Trying to follow a gene set analyisis in R by Michael Love 35k
No I can’t help with exercises. Just to be clear I’m not affiliated with Harvard and have no supported effort in relation to the edx classe…
Answer: Problems to find the pvalues via rowttests by Gordon Smyth 44k
Ordinary t-tests aren't recommended for genomic analyses because they have poor power and higher false discovery rates. Using the limma p…
Answer: How to insert a qvalues column in a dataframe with pvalues in R by Gordon Smyth 44k
Here and in a previous post, it seems you're not using recommended Bioconductor workflows for Affymetrix microarrays. If you used a standar…
Comment: Trying to follow a gene set analyisis in R by leonardorosas2001 • 0
Thank you. I hope I can still let you know if I have issues with your exercises. They are very challenging but useful! :)
Votes
Answer: Problems to find the pvalues via rowttests
A: How to use subSeq with DNAStringSet and information of GroupedIRanges?
A: How to use subSeq with DNAStringSet and information of GroupedIRanges?
Annotating GRanges with TxDb gene models using plyranges
plyranges select() when a metadata column is shared with core variable
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