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biomaRt connection sql

updated 3.8 years ago by Joan Miró ▴ 80 • written 3.8 years ago by Anand ▴ 10

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MakeOrgPackageFromNCBI NCBI SQL AnnotationForge

updated 4.8 years ago by James W. MacDonald 68k • written 4.8 years ago by chefer • 0

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R shell Python SQL Job

7.1 years ago ematsen ▴ 20

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biomedical informatics data science python SQL Job

9.1 years ago Doe, Aimee ▴ 40

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Answer: affy::rma results doesn't match with ncbi website by James W. MacDonald 68k

Please note that RMA is a method intended to normalize and summarize a set of samples rather than a single sample (it doesn't make much sen…

Comment: Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene by shepherl 4.1k

Can you try `BiocManager::install("TxDb.Mmusculus.UCSC.mm10.knownGene", type="source")`

Comment: Limma - Complex 2-way multi-level contrast with paired samples by Elizabeth • 0

Thank you very much, James! I wasn't aware of voomLmFit, and using it gave me more logical DEG. I really appreciate your time and effort!

Answer: affy::rma results doesn't match with ncbi website by ATpoint ★ 4.7k

Exact OMCIS reproduction down to the values without code and software version is borderline impossible. Either use the values as provided o…

Answer: Use of org.Rn.eg.db with GRCr8 reference genome by James W. MacDonald 68k

You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…

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Answer: Limma - Complex 2-way multi-level contrast with paired samples

Comment: Can't post a question?

Answer: Limma - Complex 2-way multi-level contrast with paired samples

Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks

Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression

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Scholar to James W. MacDonald 68k

Popular Question to Wolfgang RAFFELSBERGER ▴ 140