Bioconductor TCGA CNV

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TCGA CNV correlation between mRNA exprssion and CNV

updated 8.8 years ago by spulido99 • 0 • written 9.7 years ago by ycding ▴ 10

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cn.mops cnvtools tcga cnv

updated 9.1 years ago by Günter Klambauer ▴ 540 • written 9.1 years ago by vakul.mohanty ▴ 20

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tcga cnv gene symbol coordinate

updated 2.1 years ago by James W. MacDonald 67k • written 9.6 years ago by NS ▴ 60

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Answer: Error in get_anno_data(ontology) : ontology not supported yet... by Guido Hooiveld ★ 4.1k

Did you check the help page for the function `enrichDO`? Type `?enrichDO`. I am asking, because there it is stated that the argument `ont`…

Comment: Build error on kunpeng2 Linux aarch64 by martin.grigorov ▴ 10

Hi, There was a problem with `icu` and because of that the (r)curl library was not installed. The system/OS curl library is one version ol…

Answer: Standardization of rlog transformed counts before PCA by ATpoint ★ 4.6k

I guess you mean scaling in terms of Z-scoring? There are plenty of posts towards scaling in PCA both here on Bioconductor and in other com…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200

Also, re DMR.plot(), yes the understanding is that all DMRs from EPICv2 should be plotted in hg38. I've left that implied for the user sinc…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200

Hi Xiaofei, Thanks for this. If your data is from 450K, you'll have to call your DMRs in hg19, and then lift the DMR ranges over to hg38 p…

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Comment: Can we get beta values with DMRcate package

Answer: Can we get beta values with DMRcate package

Answer: Deseq2 Design

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