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davidnboone / tcga_brca_rnaseq

jupyter notebook; perform differential gene expression analysis using DESeq2 on TCGA RNAseq data
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Install Bioconductor apeglm? #10

Open sandra444 opened 5 years ago

sandra444 commented 5 years ago

In part 4, when running lfsShrink, I am getting this error:

Error in lfcShrink(dds, coef = "BC_subtype_TNBC_vs_HER2", type = "apeglm"): type='apeglm' requires installing the Bioconductor package 'apeglm' Traceback:

  1. lfcShrink(dds, coef = "BC_subtype_TNBC_vs_HER2", type = "apeglm")
  2. stop("type='apeglm' requires installing the Bioconductor package 'apeglm'")

I tried installing (see below) and received the following warning message:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("apeglm", version = "3.8")

Warning message in gzfile(file, mode): "cannot open compressed file 'C:\Users\sck49\AppData\Local\Temp\Rtmp6DKfSq/libloc_193_3905ec7d.rds', probable reason 'No such file or directory'" Error in gzfile(file, mode): cannot open the connection Traceback:

  1. BiocManager::install("apeglm", version = "3.8")
  2. installed.packages()
  3. saveRDS(list(base = base, value = ret0), dest)
  4. gzfile(file, mode)

Maybe I need to download something or put something in a different place?

Thanks

davidnboone commented 5 years ago

Hi Sandra,

Thanks for the comment. If you add it to the pacman call, everything should work.


if (!require("pacman")) install.packages("pacman")
pacman::p_load(apeglm, R.utils, data.table, tximport, DESeq2, biomaRt, jsonlite, BiocParallel, ggplot2, gplots, RColorBrewer, devtools, pheatmap)