J. Taroni 2018
Are the expression values of the neutrophil-associated latent variables correlated with MCPCounter (Becht, et al.) neutrophil estimates?
The correlations between the neutrophil counts and the LV expression levels are modest. (This question has come up more than once!) We think this is likely because neutrophils are terminally differentiated cells, so it is a limitation of using gene expression as a measure of neutrophil count rather than a limitation intrinsic to PLIER models or the MultiPLIER approach.
So, we’ll check to see if the two estimates from expression are highly correlated, which would lend support to this notion.
# magrittr pipe
`%>%` <- dplyr::`%>%`# plot and result directory setup for this notebook
plot.dir <- file.path("plots", "40")
dir.create(plot.dir, recursive = TRUE, showWarnings = FALSE)
results.dir <- file.path("results", "40")
dir.create(results.dir, recursive = TRUE, showWarnings = FALSE)The SLE whole blood expression data
sle.wb.file <-
file.path("data", "expression_data",
"SLE_WB_all_microarray_QN_zto_before_with_GeneSymbol.pcl")
exprs.mat <- readr::read_tsv(sle.wb.file) %>%
dplyr::select(-EntrezID) %>%
tibble::column_to_rownames("GeneSymbol") %>%
as.matrix()Parsed with column specification:
cols(
.default = col_double(),
EntrezID = col_integer(),
GeneSymbol = col_character()
)
See spec(...) for full column specifications.
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|==============================================================================| 100% 428 MBSetting row names on a tibble is deprecated.We’d like to compare this to results from 07-sle_cell_type_recount2_model.
plier.neutrophil.file <- file.path("results", "07",
"neutrophil_count_LV_both_models.tsv")
plier.neutrophil.df <- readr::read_tsv(plier.neutrophil.file)Parsed with column specification:
cols(
Sample = col_character(),
LV2 = col_double(),
LV27 = col_double(),
LV34 = col_double(),
LV87 = col_double(),
Neutrophil.Count = col_double(),
recount2_LV524 = col_double(),
recount2_LV603 = col_double(),
recount2_LV985 = col_double()
)# get cell type estimates with MCPcounter
mcp.results <-
MCPcounter::MCPcounter.estimate(expression = exprs.mat,
featuresType = "HUGO_symbols")
# we're only interested in the neutrophil counts
neutrophil.df <- reshape2::melt(mcp.results) %>%
dplyr::filter(Var1 == "Neutrophils") %>%
dplyr::select(-Var1)
colnames(neutrophil.df) <- c("Sample", "Neutrophil_estimate")joined.neutrophil.df <- dplyr::inner_join(neutrophil.df, plier.neutrophil.df,
by = "Sample")Column `Sample` joining factor and character vector, coercing into character vectorcor(joined.neutrophil.df$recount2_LV603,
joined.neutrophil.df$Neutrophil_estimate,
method = "pearson") ^ 2[1] 0.8305573readr::write_tsv(joined.neutrophil.df,
path = file.path(results.dir,
"Banchereau_MCPcounter_neutrophil_LV.tsv"))