Bioconductor Bufferedmatrix

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BufferedMatrix BufferedMatrix

10.7 years ago Emma Reick ▴ 10

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Normalization cdf probe affy BufferedMatrix Normalization cdf probe affy BufferedMatrix

14.2 years ago Radhika Ambatipudi ▴ 20

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cdf affyio oligo BufferedMatrix cdf affyio oligo BufferedMatrix

15.8 years ago Naira Naouar ▴ 140

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BiocViews cdf affyio biocViews oligo pdInfoBuilder BufferedMatrix BiocViews BiocViews cdf

updated 16.1 years ago by Seth Falcon ★ 7.4k • written 16.1 years ago by Marianne Tuefferd ▴ 10

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SNP Biobase oligo BufferedMatrix SNP Biobase oligo BufferedMatrix

updated 16.4 years ago by Benilton Carvalho ★ 4.3k • written 16.4 years ago by OLIVIERNUÑEZ ▴ 80

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Comment: Batch correction and repeated measures by Gordon Smyth 48k

Have you checked from the MDS plot that there is a visible batch effect for the repeated samples? Batch correction has lots of negative con…

Comment: Batch correction and repeated measures by Jonathan • 0

Thank you for your swift answer :)

Comment: Phenotype effect - building a contrast matrix - grouping vs interaction by Gordon Smyth 48k

I am telling you that `LS_B.vs.NL_B` is completely uninteresting. You need instead to examine `LS_Y.vs.NL_Y` and `LS_N.vs.NL_N` separately.

Answer: Batch correction and repeated measures by Gordon Smyth 48k

You should just do a standard limma analysis as recommended in the previous posts. ``` design <- model.matrix(~0 + Sample.Type + batch) i <…

Comment: DESeq2, results(dds, name = <reference>) interpretation results by Rockbar • 0

When I apply the model.matrix approach for getting the contrasts, the code > mod_mat <- model.matrix(design(dds), colData(dds)) > CondA.t…

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Answer: Batch correction and repeated measures

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