User: Marcin Jakub Kamiński

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4 years, 11 months ago
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6 years ago
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m******************@gmail.com

Posts by Marcin Jakub Kamiński

<prev • 4 results • page 1 of 1 • next >
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Comment: C: genefilter vs limma - many probes filtered
... Hello Ryan, thanks for your clear elucidation on this. Shame to admit, but after performing some additional reading I believe that my question should (at least partially) have never been asked - in limma guide it's advised to filter-out low intensities rather than low variances and more details can ...
written 5.5 years ago by Marcin Jakub Kamiński40
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Comment: C: Single-channel GenePix analysis with Limma (bg correction, normalization, weight
... Hello Gordon, Thank you for elucidation on the avereps() usage. I've misinterpreted your words as: - do average multiple replicates of same probe (across probe ID) - do not average multiple probes for same gene (across gene ID) Thank you for your support. Best regards, Marcin On Sat, Nov 16, 2 ...
written 6.0 years ago by Marcin Jakub Kamiński40
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Comment: C: Single-channel GenePix analysis with Limma (bg correction, normalization, weight
... Hello Gordon, thank you for your support. Somehow I didn't pay enough attention and thought that 'green.only' parameter shouldn't be used in my case. Now, with Elist, the analysis is much easier, thank you! However, there's a small inconvenience: I cannot simply plotDensities() for EList, because i ...
written 6.0 years ago by Marcin Jakub Kamiński40
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Single-channel GenePix analysis with Limma (bg correction, normalization, weights)
... Dear experts, I'm trying to analyze raw data from GEO GSE34571 using limma. It's 8 single-channel Agilent microarrays scanned with Genepix software to .gpr files. It's a simple design of between-group comparison including two groups, 4 replicates in each. With some help from limma guide and previou ...
microarray normalization vsn limma assign written 6.0 years ago by Marcin Jakub Kamiński40 • updated 6.0 years ago by Gordon Smyth39k

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Popular Question 5.0 years ago, created a question with more than 1,000 views. For Single-channel GenePix analysis with Limma (bg correction, normalization, weights)

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