Bioconductor Quantsmooth

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quantsmooth

updated 9.6 years ago by Jan Oosting ▴ 20 • written 9.6 years ago by bob.stephens.2005 • 0

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geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio

updated 16.8 years ago by Mike Smith ▴ 40 • written 16.8 years ago by Krys Kelly ▴ 270

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geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio

updated 16.7 years ago by Mark Dunning ▴ 320 • written 16.7 years ago by Johnstone, Alice ▴ 410

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1.2k

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geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio

updated 16.7 years ago by Mark Dunning ▴ 320 • written 16.7 years ago by Krys Kelly ▴ 270

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935

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Biobase annotate affy affyio beadarray quantsmooth beadarraySNP lumi Biobase annotate

16.7 years ago Johnstone, Alice ▴ 410

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1.2k

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Microarray Annotation geneplotter affy affyio beadarray quantsmooth beadarraySNP affy

updated 16.8 years ago by Matt Ritchie ▴ 460 • written 16.8 years ago by Keith James ▴ 10

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Clustering annotate quantsmooth Clustering annotate quantsmooth

updated 13.0 years ago by Oosting, J. PATH ▴ 550 • written 13.0 years ago by Nandini B ▴ 30

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ideogram quantsmooth GenomeGraphs ideogram quantsmooth GenomeGraphs

12.8 years ago Pete Shepard ▴ 240

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911

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quantsmooth quantsmooth

12.5 years ago Srinivas Srikanth ▴ 70

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geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio

updated 16.5 years ago by Matt Ritchie ▴ 460 • written 16.5 years ago by Elizabeth McClellan ▴ 10

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Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k

Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…

Comment: get BM error by James W. MacDonald 65k

I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…

Comment: get BM error by Fara • 0

Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…

Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k

That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…

Votes

Answer: get BM error

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

Comment: Different Shrunk Log2FC according with reference

Reproducibility issue with scran together with lapply and BiocParallel

C: SGSeq: moving toward diffex from SGSeq analysis

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