Showing : des • reset
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DESeq2 inconsistent fits depending on model design with interacting factors
des DESeq2
written 3 months ago by ▴ 10
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unreal negative log2fc values
DESeq2 des
updated 17 months ago by 68k • written 17 months ago by • 0
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9
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1.8k
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 19 months ago by 68k • written 19 months ago by • 0
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Bioinformatics student
Des DESeq2
updated 20 months ago by • 0 • written 20 months ago by • 0
2
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2
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With DESeq2 "Not full rank" Error with design
DESeq2 DEs
21 months ago feather-W • 0
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902
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Design structure
DESeq2 des
updated 3.0 years ago by 43k • written 3.1 years ago by • 0
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Design Matrix Singularity Error
DES DESIGN
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
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Matrix not full rank (time-series experiment with one group and covariates )
DESeq2 DES
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 10
8 results • Page 1 of 1
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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