Showing : DESEQ • reset
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evaluate the variable importance on genes
DESeq2 deseq
10 weeks ago Meme • 0
0
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2
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341
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Running DESeq on normalized data
deseq DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
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2
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526
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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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384
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Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 6 months ago by 41k • written 6 months ago by • 0
0
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1
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657
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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
0
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3
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900
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Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq DESeq2
updated 9 months ago by ★ 4.1k • written 9 months ago by ▴ 10
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4
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662
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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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2
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615
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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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1.3k
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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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567
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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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732
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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
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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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522
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How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 20 months ago by ★ 4.1k • written 20 months ago by • 0
3
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2
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929
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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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784
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Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 23 months ago by 41k • written 23 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 23 months ago by ★ 4.1k • written 23 months ago by • 0
2
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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 24 months ago by ▴ 10
1
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5
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1.4k
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Potential outlier/high variance
deseq DESeq2
updated 2.0 years ago by 41k • written 2.1 years ago by • 0
1
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2
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918
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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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1.6k
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Test if a gene is NOT differentially expressed in DESeq2?
DESeq2 deseq
updated 2.3 years ago by 41k • written 2.3 years ago by • 0
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2
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1.1k
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DESeqDataSet design issue
DESeq DESeq2
2.4 years ago matthew.valentine • 0
1
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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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6
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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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2
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2.3k
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
2.7 years ago • updated 2.6 years ago jbnrodriguez ▴ 10
1
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2
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987
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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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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
1
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2
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944
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metage problem with DESeq
DESeq metagene2 metagene
updated 3.1 years ago by ▴ 10 • written 3.2 years ago by ▴ 10
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3
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2.3k
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Understanding MA plot distortion
DESeq2 MAplot deseq
updated 3.2 years ago by 41k • written 3.2 years ago by • 0
0
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5
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1.8k
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ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 3.3 years ago by 41k • written 3.3 years ago by • 0
2
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12
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4.5k
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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
1
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2
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983
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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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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 4.1 years ago by ▴ 10
2
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2
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866
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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
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 4.1 years ago by 41k • written 4.1 years ago by ▴ 830
1
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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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1.2k
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how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2 deseq
4.3 years ago MANYA_BIOINFO • 0
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1
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1.3k
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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 4.5 years ago by 41k • written 4.5 years ago by ▴ 180
4
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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 4.8 years ago by ▴ 40 • written 4.8 years ago by • 0
1
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2
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894
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Filtering extraneous samples affects DESeq results. What is going on?
deseq deseq2
updated 4.8 years ago by 41k • written 4.8 years ago by • 0
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0
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946
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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
3
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12
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1.6k
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Why did I get NA p-values in DESeq with continuous variable?
deseq2 p-value continuous deseq
5.2 years ago ariel ▴ 20
2
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3
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1.9k
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DESeq2 count outlier replacement from Cook's threshold
deseq2 deseq rnaseq outliers count outliers
updated 5.4 years ago by 41k • written 5.4 years ago by ▴ 10
0
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1
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1.0k
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Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
0
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3
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1.2k
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Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
5.6 years ago Ben ▴ 50
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7
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3.9k
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DESeq2 install problem
deseq
updated 5.6 years ago by 41k • written 5.6 years ago by • 0
5
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7
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3.6k
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Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 5.6 years ago by 41k • written 5.6 years ago by ▴ 10
50 results • Page 1 of 1
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Replies
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Comment: Help with running egsea() by James W. MacDonald 65k
I don't understand the last question, but do look at the msigdb.gsets argument to `buildIdx` in the help page for that function.
Answer: Help with running egsea() by James W. MacDonald 65k
There are no arguments to `egsea.base`, as it is meant only as a helper function to return the different methods. In addition, if you are u…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I am working with mouse data. I don't know how to do this, but I will go through it. Can you help me with the second question? how do we …
Comment: [Mfuzz] Error in cmeans(exprs(eset) by Caio • 0
You can have this problem (lines with variance equal to zero) when you run experiments and obtain the data with more samples and use fewer …
Votes
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Answer: How to save the DEXSeq results
Answer: Help with running egsea()
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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