Bioconductor Readaffy

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1.2k

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affycoretools ReadAffy Biobase phenoData affy

updated 3.0 years ago by James W. MacDonald 64k • written 3.0 years ago by bastien_chassagnol • 0

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497

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affyio.rdb ReadAffy

updated 4.6 years ago by James W. MacDonald 64k • written 4.6 years ago by na396 • 0

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2.2k

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readaffy frma affy package installation hgu133a

5.7 years ago Chris Mancuso • 0

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3.2k

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affy normalization affymetrix limma Readaffy

8.2 years ago florent.dumont • 0

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2.2k

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CEL RAW geoquery readaffy

updated 9.1 years ago by Sean Davis 21k • written 9.1 years ago by PyPer ▴ 20

5 results • Page 1 of 1

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Answer: Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DE by James W. MacDonald 64k

The short answer is that you don't. `tximport` is meant to summarize transcript abundance estimates at the gene level, and as you might ima…

Comment: Inconsistent results in DiffBind by ATpoint ★ 3.6k

One is the "raw" logFCs, not corrected for the standard error of the logFCs, the other one the shrunken logFCs from DESeq2 lfcShrink, "corr…

Answer: Can't download Bioconductor by James W. MacDonald 64k

[You need to update][1]. [1]: https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html#basic-use

Comment: Can't download Bioconductor by ATpoint ★ 3.6k

Please see especially the 1st and 2nd point in https://www.bioconductor.org/help/support/posting-guide/#keypoints

Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance by Michael Love 41k

With 3 vs 3, when one sample increases from 50 to 5000, this can lead to rejection of null hypothesis. I'm not surprised with the above cou…

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Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance

Answer: What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)

Answer: WGCNA documentation not available

Comment: Can the limma package be applied to Log2 RUV-normalized data?

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