Bioconductor RNAseq

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limma limma voom rnaseq_analysis DEG

6.7 years ago • updated 5.7 years ago SPbeginner • 0

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rnaseq_analysis KEGG nonmodel species

updated 6.2 years ago by James W. MacDonald 67k • written 6.2 years ago by laural710 • 0

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sequencing rnaseq_analysis

6.8 years ago alemutak • 0

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rnaseq_analysis

7.5 years ago fakhter1 • 0

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rnaseq_analysis

updated 8.2 years ago by Gordon Smyth 51k • written 8.2 years ago by kjo ▴ 70

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deseq2 rnaseq_analysis variancestabilizingtransformation confounders

updated 8.5 years ago by Michael Love 42k • written 8.5 years ago by ompandey ▴ 10

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limma RNAseq_Analysis model.matrix

updated 9.5 years ago by Aaron Lun ★ 28k • written 9.5 years ago by anver • 0

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Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k

Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…

Comment: Identifying potentially associated gene set to drug response using GSVA by Kent • 0

Hi @robertc thanks for the reply. I should have explained to you the context first. I am testing over a hundred drugs on patient samples (s…

Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification by James W. MacDonald 67k

You can easily answer this question yourself. ``` > library(BiocPkgTools) Loading required package: htmlwidgets > depdf <- buildPkgDe…

Answer: HilBertVis install error by James W. MacDonald 67k

It appears you have compiler flags set that preclude you from compiling (-Werror=format-security). If I install `HilbertVis` on my work box…

Comment: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael for quick reply. Actually, I also questioned this but later i saw this issue happens within another cluster and different c…

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A: TopGO: How to retrieve the gene list related to a GO ID ?

A: Error in DESeqDataSet : some values in assay are not integers

A: correcting the batch effects in Limma and SVA

A: Using of limma moderated t-test with "corrected" expression matrix resulting fr

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