Bioconductor NCBI GEO

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NCBI GEO

updated 4.0 years ago by SAn • 0 • written 8.8 years ago by maedakus ▴ 10

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geoquery ncbi geo biobase

6.0 years ago cschot3 • 0

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limma differential gene expression ncbi geo affymetrix microarrays

updated 6.0 years ago by Aaron Lun ★ 28k • written 6.1 years ago by Francesca McGrath • 0

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frma barcode geneexpression gsm ncbi geo

updated 7.0 years ago by Matthew McCall ▴ 830 • written 7.0 years ago by diana.elassal • 0

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limma microarray bioconductor ncbi geo

updated 7.9 years ago by Gordon Smyth 51k • written 7.9 years ago by kevin.m.hao ▴ 10

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4.3k

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geoquery ncbi geo geo data

8.0 years ago fongchunchan ▴ 30

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Comment: Deseq2 res Function by James W. MacDonald 67k

In addition to Mike's comment, do note that if you are generating a heatmap based on the set of significant genes, the direction of your co…

Answer: Struggle with the replicates of epic array data by James W. MacDonald 67k

You shouldn't be using beta values for a linear model that assumes a unimodal, untruncated distribution (beta values are strictly on (0-1) …

Comment: Identifying potentially associated gene set to drug response using GSVA by Robert Castelo ★ 3.4k

So, if I understand correctly, you derived GSVA scores from gene sets corresponding somehow to drugs in your RNA-seq data. Since GSVA score…

Answer: Deseq2 res Function by Michael Love 43k

> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…

Answer: ANOVA like approach of edgeR by Gordon Smyth 51k

You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…

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Comment: Is it recommended to analyze different tissues together when using edgeR

Answer: Deseq2 res Function

Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification

Answer: ANOVA like approach of edgeR

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