User: M.Gierlinski

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2 years, 9 months ago
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Posts by M.Gierlinski

<prev • 7 results • page 1 of 1 • next >
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Large example data with Bioconductor package
... I'm writing an R package I intend to submit to Bioconductor. The aim of the package is to analyse high throughput proteomics data, starting from the MaxQuant evidence file. I feel it is necessary to show step-by-step examples of such analysis in a vignette. However, this would require attaching larg ...
package written 22 days ago by M.Gierlinski0 • updated 22 days ago by shepherl ♦♦ 510
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Comment: C: One-condition limma test
... This makes sense. Certainly, log-ratios are more symmetric (as mentioned by James below) and the null hypothesis of zero allows for the intercept-only model. Thanks!   ...
written 6 weeks ago by M.Gierlinski0
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One-condition limma test
... Consider an experiment (e.g. proteomics) producing ratios. Our null hypothesis is that each ratio is one. In this particular example, I have a data table with n rows (peptides) and m columns (replicates). I would like to use limma to do a differential expression of each peptide versus a constant of ...
limma t-test written 6 weeks ago by M.Gierlinski0 • updated 6 weeks ago by James W. MacDonald45k
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Comment: C: Goseq problem with "missing value"
... OK, this helped! I updated goseq to version 1.18.0 and the error disappeared. Thanks a lot, Marek ...
written 2.8 years ago by M.Gierlinski0
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Goseq problem with "missing value"
... I'm running goseq on a sequence of bootstraps where a DE test is performed on a random selection of replicates. THis way, I have a constant list of background genes and a selection of significant genes which is slightly changing from bootstrap to bootstrap. goseq works nicely on most of these bootst ...
goseq written 2.8 years ago by M.Gierlinski0 • updated 2.8 years ago by Nadia Davidson260
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Answer: A: Goseq and yeast
... Thanks, Nadia. This solved the problem! Cheers, Marek ...
written 2.8 years ago by M.Gierlinski0
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Goseq and yeast
... We are trying to use goseq on our yeast data, but there is a problem with the yeast database. I managed to create a pwf object with nullp(), but the next step fails: > pwf = nullp(gene.vector, "sacCer3", "ensGene") Can't find sacCer3/ensGene length data in genLenDataBase... Trying to download f ...
yeast goseq written 2.8 years ago by M.Gierlinski0

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