Biostar Read.maimages

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limma read.maimages normalization preprocessing

updated 3.5 years ago by Gordon Smyth 43k • written 3.5 years ago by marviedemit ▴ 10

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limma read.maimages

updated 3.7 years ago by Gordon Smyth 43k • written 14.5 years ago by Lakshmanan Iyer ▴ 250

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differential gene expression limma read.maimages

updated 6.1 years ago by Gordon Smyth 43k • written 6.1 years ago by SSK ▴ 10

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limma bioconductor read.maimages agilent 8x60K

6.3 years ago wd ▴ 30

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Comment: DESeq2: Variable Importance by lolol • 0

Ah yes, I see the deviance now in mcols. Would I use this to calculate the pseudo R-squared (McFaddens), comparing each model with a single…

Answer: How to do annotation with Limma by Guido Hooiveld ★ 3.0k

For the HTA2.0 arrays should not use `hgu95av2.db`, which is the annotation library for the, ehh, human U95 set of Affymetrix arrays! You s…

Comment: DESeq2: Variable Importance by Michael Love 33k

Yes, `deviance` is an output in the `mcols`, so you could rotate through variables, excluding them in the LRT. Or you could use the other p…

Answer: Hard coding in DiffBind DBA.R line 968 by Rory Stark ★ 3.9k

Thank you for noticing and reporting this potential issue relating to the minimum number of sample replicates required to form a contrast. …

Comment: DESeq2: Variable Importance by lolol • 0

When you say observing the deviance, you mean utilizing the likelihood ratio test with the reduced model (exclude the last variable). Am I …

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Answer: How to do annotation with Limma

Final List of Deprecated Packages for Bioc3.13

Answer: RNAseq : identical sample-sample distances after using limma::removeBatchEffect

Comment: Use of arrayWeights with two treatment groups

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Popular Question to Guido Hooiveld ★ 3.0k