QC for DC panel
library(flowCore)
library(flowWorkspace)
# library(cytoqc)
devtools::load_all()
path <- "~/remote/fh/fast/gottardo_r/mike_working/lyoplate_out/parsed"
centers <- c('BIIR','CIMR','Miami','NHLBI','Stanford','UCLA','Yale')
Load gs
panel <- "DC"
gslist <- sapply(centers, function(center) {
message("Center: ", center)
gs <- load_gs(file.path(path, center, panel), select = 1)
})
cqc_data <- cqc_gs_list(gslist)
Check
check_res <- cqc_check(cqc_data, "panel", by = "marker")
check_res
|
marker
|
group 1(n=1)
|
group 2(n=1)
|
group 3(n=1)
|
group 4(n=1)
|
group 5(n=1)
|
group 6(n=1)
|
group 7(n=1)
|
|
CD11c
|
<PE-Cy7 YG-A>
|
<PE-Cy7-A>
|
<PE Cy7 YG-A>
|
<PE-Cy7-A>
|
N/A
|
<PE-Cy7-A>
|
N/A
|
|
CD11C
|
N/A
|
N/A
|
N/A
|
N/A
|
<PE-Cy7-A>
|
N/A
|
N/A
|
|
CD11c PE-Cy7
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
<G780-A>
|
|
CD123
|
<PerCP-Cy5-5-A>
|
<PerCP-Cy5-5-A>
|
<PerCP-Cy5-5-A>
|
<PerCP-Cy5-5-A>
|
<PerCP-Cy5-5-A>
|
<PerCP-Cy5-5-A>
|
N/A
|
|
CD123 PerCP-Cy55
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
<B710-A>
|
|
CD14
|
<Pacific Blue-A>
|
<Pacific Blue-A>
|
<Pacific Blue-A>
|
<V450-A>
|
<BD Horizon V450-A>
|
<V450-A>
|
N/A
|
|
CD14 V450
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
<V450-A>
|
|
CD16
|
<APC-A>
|
<APC-A>
|
<APC-A>
|
<APC-A>
|
<APC-A>
|
<APC-A>
|
N/A
|
|
CD16 APC
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
<R660-A>
|
|
CD3_CD19_CD20
|
<APC-Cy7-A>
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
|
CD3+19+20
|
N/A
|
N/A
|
N/A
|
N/A
|
<APC-H7-A>
|
N/A
|
N/A
|
|
CD3+CD19+CD20
|
N/A
|
<APC-Cy7-A>
|
N/A
|
<APC-Cy7-A>
|
N/A
|
N/A
|
N/A
|
|
CD3+CD19+CD20+
|
N/A
|
N/A
|
<APC-Cy7-A>
|
N/A
|
N/A
|
N/A
|
N/A
|
|
CD3CD19CD20
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
<APC-H7-A>
|
N/A
|
|
CD56
|
<PE YG-A>
|
<PE-A>
|
<PE-A>
|
<PE-A>
|
<PE-A>
|
<PE-A>
|
N/A
|
|
CD56 PE
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
<G560-A>
|
|
HLA DR
|
N/A
|
<Am Cyan-A>
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
|
HLA-DR
|
N/A
|
N/A
|
<AmCyan-A>
|
<V500-A>
|
<BD Horizon V500-A>
|
<V500-A>
|
N/A
|
|
HLA-DR V500
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
<V545-A>
|
|
HLADR
|
<AmCyan-A>
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
|
Lineage APC-H7
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
<R780-A>
|
|
LIVE
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
<FITC-A>
|
N/A
|
|
LIVE DEAD
|
N/A
|
N/A
|
N/A
|
N/A
|
<FITC-A>
|
N/A
|
N/A
|
|
Live Dead FITC
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
<B515-A>
|
|
Live Green
|
N/A
|
N/A
|
<FITC-A>
|
<FITC-A>
|
N/A
|
N/A
|
N/A
|
|
LIVE_GREEN
|
<Alexa Fluor 488-A>
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
|
Live/Dead
|
N/A
|
<FITC-A>
|
N/A
|
N/A
|
N/A
|
N/A
|
N/A
|
cqc_match(check_res, ref = 1)
## Error in (function (df, ...) : marker is not consistent across panel groups!Please standardize it first!
standardize marker first
check_res <- cqc_check(cqc_data, "marker")
match_res <- cqc_match(check_res, ref = 7, max.dist = 0.6)
match_res <- cqc_update_match(match_res, c("Lineage APC-H7" = "CD3CD19CD20"))
cqc_fix(match_res)
cqc_check(cqc_data, "marker")
|
group_id
|
nGatingSet
|
marker
|
|
1
|
7
|
CD11c, CD123, CD14, CD16, CD3CD19CD20, CD56, HLA-DR, LIVE
|
Check
check_res <- cqc_check(cqc_data, "panel", by = "marker")
check_res
|
marker
|
group 1(n=1)
|
group 2(n=1)
|
group 3(n=1)
|
group 4(n=1)
|
group 5(n=1)
|
group 6(n=1)
|
group 7(n=1)
|
|
CD11c
|
<PE-Cy7 YG-A>
|
<PE-Cy7-A>
|
<PE Cy7 YG-A>
|
<PE-Cy7-A>
|
<PE-Cy7-A>
|
<PE-Cy7-A>
|
<G780-A>
|
|
CD123
|
<PerCP-Cy5-5-A>
|
<PerCP-Cy5-5-A>
|
<PerCP-Cy5-5-A>
|
<PerCP-Cy5-5-A>
|
<PerCP-Cy5-5-A>
|
<PerCP-Cy5-5-A>
|
<B710-A>
|
|
CD14
|
<Pacific Blue-A>
|
<Pacific Blue-A>
|
<Pacific Blue-A>
|
<V450-A>
|
<BD Horizon V450-A>
|
<V450-A>
|
<V450-A>
|
|
CD16
|
<APC-A>
|
<APC-A>
|
<APC-A>
|
<APC-A>
|
<APC-A>
|
<APC-A>
|
<R660-A>
|
|
CD3CD19CD20
|
<APC-Cy7-A>
|
<APC-Cy7-A>
|
<APC-Cy7-A>
|
<APC-Cy7-A>
|
<APC-H7-A>
|
<APC-H7-A>
|
<R780-A>
|
|
CD56
|
<PE YG-A>
|
<PE-A>
|
<PE-A>
|
<PE-A>
|
<PE-A>
|
<PE-A>
|
<G560-A>
|
|
HLA-DR
|
<AmCyan-A>
|
<Am Cyan-A>
|
<AmCyan-A>
|
<V500-A>
|
<BD Horizon V500-A>
|
<V500-A>
|
<V545-A>
|
|
LIVE
|
<Alexa Fluor 488-A>
|
<FITC-A>
|
<FITC-A>
|
<FITC-A>
|
<FITC-A>
|
<FITC-A>
|
<B515-A>
|
Match
match_res <- cqc_match(check_res, ref = 1)
match_res
|
marker
|
Ref group
|
group 2(n=1)
|
group 3(n=1)
|
group 4(n=1)
|
group 5(n=1)
|
group 6(n=1)
|
group 7(n=1)
|
|
CD11c
|
<PE-Cy7 YG-A>
|
<PE-Cy7-A>
|
<PE Cy7 YG-A>
|
<PE-Cy7-A>
|
<PE-Cy7-A>
|
<PE-Cy7-A>
|
<G780-A>
|
|
CD123
|
<PerCP-Cy5-5-A>
|
<PerCP-Cy5-5-A>
|
<PerCP-Cy5-5-A>
|
<PerCP-Cy5-5-A>
|
<PerCP-Cy5-5-A>
|
<PerCP-Cy5-5-A>
|
<B710-A>
|
|
CD14
|
<Pacific Blue-A>
|
<Pacific Blue-A>
|
<Pacific Blue-A>
|
<V450-A>
|
<BD Horizon V450-A>
|
<V450-A>
|
<V450-A>
|
|
CD16
|
<APC-A>
|
<APC-A>
|
<APC-A>
|
<APC-A>
|
<APC-A>
|
<APC-A>
|
<R660-A>
|
|
CD3CD19CD20
|
<APC-Cy7-A>
|
<APC-Cy7-A>
|
<APC-Cy7-A>
|
<APC-Cy7-A>
|
<APC-H7-A>
|
<APC-H7-A>
|
<R780-A>
|
|
CD56
|
<PE YG-A>
|
<PE-A>
|
<PE-A>
|
<PE-A>
|
<PE-A>
|
<PE-A>
|
<G560-A>
|
|
HLA-DR
|
<AmCyan-A>
|
<Am Cyan-A>
|
<AmCyan-A>
|
<V500-A>
|
<BD Horizon V500-A>
|
<V500-A>
|
<V545-A>
|
|
LIVE
|
<Alexa Fluor 488-A>
|
<FITC-A>
|
<FITC-A>
|
<FITC-A>
|
<FITC-A>
|
<FITC-A>
|
<B515-A>
|
Fix
cqc_fix(match_res)
cqc_check(cqc_data, "panel")
|
channel
|
group 1(n=7)
|
|
<Alexa Fluor 488-A>
|
LIVE
|
|
<AmCyan-A>
|
HLA-DR
|
|
<APC-A>
|
CD16
|
|
<APC-Cy7-A>
|
CD3CD19CD20
|
|
<Pacific Blue-A>
|
CD14
|
|
<PE YG-A>
|
CD56
|
|
<PE-Cy7 YG-A>
|
CD11c
|
|
<PerCP-Cy5-5-A>
|
CD123
|
``