Showing : snpchip • reset
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Support for MouseDivGeno arrays in Bioconductor
snpchip microarray affy
10.8 years ago Sean Davis 21k
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2
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1.8k
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Can my problem be addressed with Bioconductor?
Genetics GOstats SNPchip topGO Genetics GOstats SNPchip topGO
updated 11.6 years ago by 68k • written 11.6 years ago by ★ 13k
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genotyping output files
PROcess SNPchip crlmm PROcess SNPchip crlmm
14.0 years ago Rafiq S. ▴ 20
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1.2k
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Possible bug in SNPchip
Proteomics SNPchip Proteomics SNPchip
updated 14.2 years ago by ▴ 250 • written 14.2 years ago by ▴ 110
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Bioconductor / plotting SNPs, runs of homozygosity
SNP geneplotter SNPchip SNP geneplotter SNPchip
updated 15.6 years ago by 6.7k • written 15.6 years ago by ▴ 40
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Question about using oligo and SNPchip for copy number analysis
SNP Cancer graph oligo SNPchip oligoClasses VanillaICE crlmm SNP Cancer graph oligo
16.7 years ago Min-Han Tan ▴ 40
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2.1k
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how to put together 600 files from the 5.0 Affy SNPchip
SNP SNPchip SNP SNPchip
17.2 years ago Laura Rodriguez Murillo ▴ 60
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1
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1.7k
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[Bioc-devel] SNPscan -> SNPchip
SNP Annotation Yeast Biobase SNPchip SNP Annotation Yeast Biobase SNPchip
updated 19.2 years ago by ▴ 250 • written 19.2 years ago by ▴ 170
8 results • Page 1 of 1
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Answer: lfc shrinkage estimator in DESeq2 by plumsgorillas • 0
You are on the right track. In DESeq2, raw log2 fold changes are often noisy and can be misleading, especially for genes with low counts. A…
Answer: Array weights in dpcDE by Gordon Smyth 53k
The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. However,…
Answer: lfc shrinkage estimator in DESeq2 by Michael Love 43k
Try the vignette which has a lot of information on these type of questions.
Comment: limpa analysis advice by Gordon Smyth 53k
The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …
Comment: limpa analysis advice by SamGG ▴ 360
Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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