Concatenation & Normalization
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.
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.
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_ff, e.g. 111000, as its unique identifier.
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.
flowFrame with 5000 spill-affected
multiplexed cells and 39 measurement parameters.
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.
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.
a 2 column
data.frame that contains each marker's
column name in the FCS file, and its targeted protein marker.
data.frame where each row corresponds to a sample,
and with columns describing the experimental design.
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 email@example.com
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).
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### 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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