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Pathway visualization with pathview doesn't color some genes which in fact appear on the dataset
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6 hours ago Emilia • 0 • updated 5 hours ago James W. MacDonald 55k
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biomaRt "longer object length is not a multiple of shorter object length"
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Different contrast coding strategies in DESeq2 produce slightly different output?
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3 days ago • updated 11 hours ago Ben • 0
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4.6 years ago Christoph • 10 • updated 17 hours ago Michael Love 30k
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How to add a column to metadata in SummarizedExperiment for DESeq2 type objects?
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4 days ago • updated 1 day ago Nick • 0
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2.8 years ago jinxinhao1988 • 0 • updated 2 days ago El • 0
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champ.DMP finds different probes in A-vs-B and B-vs-A analysis
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2 days ago Ricardo • 0 • updated 2 days ago Yuan Tian • 180
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4 days ago • updated 3 days ago Mike • 10
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Perform a biplot from pcaData and coldata in DESeq2, maybe PCAtools?
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4 days ago ecg1g15 • 0 • updated 4 days ago Kevin Blighe 2.1k
263 results • Page 1 of 6
Recent ...
Replies
Comment: Pathway visualization with pathview doesn't color some genes which in fact appea by James W. MacDonald 55k
You need to provide a self-contained example that other people can run. You could for example provide the output from running `dput` on you…
Answer: biomaRt "longer object length is not a multiple of shorter object length" by James W. MacDonald 55k
The `rownames` of your count data are 1:N, so you should have no expectation that any Ensembl Gene ID should match. Also what is `seqdata`?…
Comment: How to retrieve genomic coordinates for a list of entrezID and their respective by James W. MacDonald 55k
And do note that the names of the `GRangesList` you get from `cdsBy` are the NCBI Gene IDs (what you are calling EntrezGene IDs). So you co…
Answer: How to retrieve genomic coordinates for a list of entrezID and their respective by James W. MacDonald 55k
The TSS is the first base of the transcript, and genes can have multiple transcripts. And the NCBI Gene ID pertains to genes, not transcrip…
Comment: Different contrast coding strategies in DESeq2 produce slightly different output by Ben • 0
Hi @mikelove! Thanks for your answer. You are right, the values are all zero for the specified contrast - I checked. I expect that expla…
Votes
Answer: DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Different contrast coding strategies in DESeq2 produce slightly different output
Answer: Different contrast coding strategies in DESeq2 produce slightly different output
A: [DESeq2] time series strain-specific differences over time
Comment: Normalise to a housekeeping gene in DESEq2
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