Last updated: 2025-06-03
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The MCF-7 data set from Sanford et al eLife paper could be a great data set for illustrating many of the ideas behind NMF analysis of single-cell data (even though it is actually a bulk RNA-seq data set). This paper analyzed the transcriptional response of human MCF-7 cells to retinoic acid and TGF-\(\beta\), applied individually and in combination. The data were downloaded from GEO accession GSE152749.
The following abbreviations were used in analysis: EtOH = ethanol; RA = retinoic acid; TGFb = TGF-\(\beta\).
Load packages used to process the data, perform the analyses, and create the plots.
library(rsvd)
library(fastglmpca)
library(fastTopics)
library(flashier)
library(data.table)
library(GEOquery)
library(singlecelljamboreeR)Set the seed for reproducibility:
set.seed(1)Load the RNA-seq counts:
counts <- fread("../data/GSE152749_raw_counts_GRCh38.p13_NCBI.tsv.gz",
sep = "\t",header = TRUE,stringsAsFactors = FALSE)
class(counts) <- "data.frame"
rownames(counts) <- counts$GeneID
counts <- counts[,-1]
counts <- as.matrix(counts)
storage.mode(counts) <- "double"
counts <- t(counts)
ids <- rownames(counts)Load the gene information:
genes <- fread("../data/Human.GRCh38.p13.annot.tsv.gz",sep = "\t",
header = TRUE,stringsAsFactors = FALSE)
class(genes) <- "data.frame"
genes <- genes[1:10]
genes <- transform(genes,
GeneType = factor(GeneType),
Status = factor(Status))Load the sample information:
geo <- getGEO(filename = "../data/GSE152749_family.soft.gz")
samples <- data.frame(id = names(GSMList(geo)),
treatment = sapply(GSMList(geo),
function (x) Meta(x)$title))
samples <- samples[ids,]
rownames(samples) <- NULL
samples <- transform(samples,
EtOH = grepl("EtOH",treatment,fixed = TRUE),
RA = grepl("RA",treatment,fixed = TRUE),
TGFb = grepl("TGFb",treatment,fixed = TRUE))
samples$label <- "EtOH"
samples[samples$RA,"label"] <- "RA"
samples[samples$TGFb,"label"] <- "TGFb"
samples[with(samples,RA & TGFb),"label"] <- "RA+TGFb"
samples <- transform(samples,
label = factor(label,c("EtOH","RA","TGFb","RA+TGFb")))
sessionInfo()
# R version 4.3.3 (2024-02-29)
# Platform: aarch64-apple-darwin20 (64-bit)
# Running under: macOS 15.4.1
#
# Matrix products: default
# BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
# LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
#
# locale:
# [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#
# time zone: America/Chicago
# tzcode source: internal
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] singlecelljamboreeR_0.1-3 GEOquery_2.70.0
# [3] Biobase_2.62.0 BiocGenerics_0.48.1
# [5] data.table_1.15.2 flashier_1.0.55
# [7] ebnm_1.1-34 fastTopics_0.7-24
# [9] fastglmpca_0.1-108 rsvd_1.0.5
#
# loaded via a namespace (and not attached):
# [1] distr_2.9.3 pbapply_1.7-2 rlang_1.1.5
# [4] magrittr_2.0.3 git2r_0.33.0 horseshoe_0.2.0
# [7] compiler_4.3.3 vctrs_0.6.5 reshape2_1.4.4
# [10] daarem_0.7 quadprog_1.5-8 stringr_1.5.1
# [13] pkgconfig_2.0.3 crayon_1.5.2 fastmap_1.1.1
# [16] utf8_1.2.4 promises_1.2.1 rmarkdown_2.26
# [19] tzdb_0.4.0 purrr_1.0.2 xfun_0.42
# [22] cachem_1.0.8 trust_0.1-8 jsonlite_1.8.8
# [25] progress_1.2.3 later_1.3.2 irlba_2.3.5.1
# [28] parallel_4.3.3 prettyunits_1.2.0 R6_2.5.1
# [31] bslib_0.6.1 stringi_1.8.3 RColorBrewer_1.1-3
# [34] SQUAREM_2021.1 limma_3.58.1 jquerylib_0.1.4
# [37] Rcpp_1.0.12 knitr_1.45 R.utils_2.12.3
# [40] readr_2.1.5 httpuv_1.6.14 Matrix_1.6-5
# [43] splines_4.3.3 tidyselect_1.2.1 yaml_2.3.8
# [46] lattice_0.22-5 tibble_3.2.1 plyr_1.8.9
# [49] evaluate_1.0.3 Rtsne_0.17 RcppParallel_5.1.10
# [52] startupmsg_0.9.6.1 xml2_1.3.6 pillar_1.9.0
# [55] whisker_0.4.1 plotly_4.10.4 softImpute_1.4-1
# [58] generics_0.1.3 rprojroot_2.0.4 invgamma_1.1
# [61] truncnorm_1.0-9 hms_1.1.3 ggplot2_3.5.0
# [64] munsell_0.5.0 scales_1.3.0 ashr_2.2-66
# [67] gtools_3.9.5 RhpcBLASctl_0.23-42 glue_1.8.0
# [70] scatterplot3d_0.3-44 lazyeval_0.2.2 tools_4.3.3
# [73] fs_1.6.5 cowplot_1.1.3 grid_4.3.3
# [76] tidyr_1.3.1 colorspace_2.1-0 sfsmisc_1.1-18
# [79] deconvolveR_1.2-1 cli_3.6.4 Polychrome_1.5.1
# [82] workflowr_1.7.1 fansi_1.0.6 mixsqp_0.3-54
# [85] viridisLite_0.4.2 dplyr_1.1.4 uwot_0.2.3
# [88] gtable_0.3.4 R.methodsS3_1.8.2 sass_0.4.9
# [91] digest_0.6.34 ggrepel_0.9.5 htmlwidgets_1.6.4
# [94] R.oo_1.26.0 htmltools_0.5.8.1 lifecycle_1.0.4
# [97] httr_1.4.7 statmod_1.5.0 MASS_7.3-60.0.1