User: mwesthues

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mwesthues0
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Posts by mwesthues

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Difference between one-stage and two-stage analyses of multiple microarray exper
... Thanks for your answer! That sounds reasonable. My assumption is that there is no option to treat such experimental effects in limma as random or am I wrong about that? Would you change anything about my one-stage approach or does this also seem correct to you? ...
written 3.8 years ago by mwesthues0
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Comment: C: Difference between one-stage and two-stage analyses of multiple microarray exper
... Yes, I am referring to the log-ratio between a given RNA source and my chosen reference for each gene. ...
written 3.8 years ago by mwesthues0
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Difference between one-stage and two-stage analyses of multiple microarray experiments in limma
... I have multiple two-color microarray experiments, analyzed with the same technology, that are  connected through common genotypes. I want to compute best linear unbiased estimates  (BLUEs)/adjusted values for each RNA source across all experiments. I have tried a combined analysis  in limma in a sin ...
limma R limma design matrix written 3.8 years ago by mwesthues0 • updated 3.8 years ago by Gordon Smyth37k
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Comment: C: Correct setup of a design matrix for a two-color, interwoven microarray loop des
... Many thanks for the clarification! I will try as you have suggested.     ...
written 3.8 years ago by mwesthues0
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Comment: C: Correct setup of a design matrix for a two-color, interwoven microarray loop des
... I will try a separate channel analysis of the two-color data and check whether that works for me. Regarding the direct two-color design, I am still lacking the understanding of the set-up of the design matrix. In the limma User's guide (p.38 & p.54) a common reference, which I do not have, is ...
written 3.8 years ago by mwesthues0
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Comment: C: Correct setup of a design matrix for a two-color, interwoven microarray loop des
... Thanks for your helpful remarks! I have added information on the experimental design and the goal of our analysis. 1. We do not have any biological replicates, just technical replicates of RNA sources. 2. Our goal is to compute "adjusted" gene expression values for each RNA source.   ...
written 3.8 years ago by mwesthues0
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Correct setup of a design matrix for a two-color, interwoven microarray loop design with dye swaps
... This question has migrated from https://www.biostars.org/p/153362/ to this website. I am looking for the correct way to set up a design matrix for a two-color. interwoven microarray loop design with dye swaps. So far, I have only found thoroughly described/discussed examples that use a common refer ...
microarray limma limma design matrix two-colour dye-swap written 3.8 years ago by mwesthues0 • updated 3.8 years ago by James W. MacDonald50k

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