data | R Documentation |
Concatenation & Normalization
raw_data
a flowSet
with 3 experiments, each containing 2'500 raw
measurements with a variation of signal over time. Samples were mixed
with DVS beads capture by mass channels 140, 151, 153, 165 and 175.
Debarcoding
sample_ff
a flowFrame
following a 6-choose-3 barcoding scheme
where mass channels 102, 104, 105, 106, 108, and 110 were used for labeling
such that each of the 20 individual barcodes are positive for exactly 3
out of the 6 barcode channels.
sample_key
a data.frame
of dimension 20 x 6 with sample names as row and
barcode masses as column names. Contains a binary code of length 6 for each
sample in sample_ff
, e.g. 111000, as its unique identifier.
Compensation
ss_exp
a flowFrame
with 20'000 events.
Contains 36 single-antibody stained controls where beads were stained
with antibodies captured by mass channels 139, 141 through 156, and
158 through 176, respectively, and pooled together.
mp_cells
a flowFrame
with 5000 spill-affected
multiplexed cells and 39 measurement parameters.
isotope_list
a named list of isotopic compositions for all elements within 75 through 209 u corresponding to the CyTOF mass range at the time of writing.
Differential Analysis
PBMC_fs
a flowSet
with PBMCs samples from 6 patients. For each sample,
the expression of 10 cell surface and 14 signaling markers was measured
before (REF) and upon BCR/FcR-XL stimulation (BCRXL) with B cell receptor/
Fc receptor crosslinking for 30', resulting in a total of 12 samples.
PBMC_panel
a 2 column data.frame
that contains each marker's
column name in the FCS file, and its targeted protein marker.
PBMC_md
a data.frame
where each row corresponds to a sample,
and with columns describing the experimental design.
merging_table
a 20 x 2 table with "old_cluster" IDs and "new_cluster" labels to exemplify manual cluster merging and cluster annotation.
see descriptions above.
Helena L Crowell helena.crowell@uzh.ch
Bodenmiller, B., Zunder, E.R., Finck, R., et al. (2012). Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators. Nature Biotechnology 30(9): 858-67.
Coursey, J.S., Schwab, D.J., Tsai, J.J., Dragoset, R.A. (2015). Atomic weights and isotopic compositions, (available at http://physics.nist.gov/Comp).
### example data for concatenation & normalization:
# raw measurement data
data(raw_data)
### example data for debarcoding:
# 20 barcoded samples
data(sample_ff)
# 6-choose-3 barcoding scheme
data(sample_key)
### example data for compensation:
# single-stained control samples
data(ss_exp)
# multiplexed cells
data(mp_cells)
### example data for differential analysis:
# REF vs. BCRXL samples
data(PBMC_fs)
# antigen panel & experimental design
data(PBMC_panel, PBMC_md)
# exemplary manual merging table
data(merging_table)
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