Showing : MassSpectrometryData • reset
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R for Mass Spectrometry: Precursor Scan Number lost when converting .wiff to .mzML?
Proteomics RforProteomics ProteomicsWorkflow Spectra MassSpectrometryData
updated 17 months ago by 1.6k • written 17 months ago by • 0
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Job: Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData RNA DifferentialExpression
2.3 years ago António Miguel de Jesus Domingues ▴ 510
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1.1k
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Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 2.4 years ago by 52k • written 2.4 years ago by • 0
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How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 3.4 years ago by • 0 • written 3.4 years ago by • 0
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How can I convert the "Majority protein IDs" to "Gene names" (example below shown)?
MassSpectrometryData Proteome Database DEP
3.8 years ago tpm • 0
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
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C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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