getMatSubtractedBaseline.RdExtract an assay from a SummarizedExperiment, and for each feature
subtract the average value across a set of reference/background/baseline
samples, and add the average across all the baseline samples to retain
information about overall abundance. Typically used to adjust for varying
baselines between batches, when a reference sample is included in each batch.
getMatSubtractedBaseline(sce, assayName, baselineGroup, sceFull)A SummarizedExperiment object. The colData of the
object must have at least columns named 'group' and 'batch'.
The name of the assay to extract from sce.
The value of the 'group' column of
colData(sceFull) that corresponds to the baseline/reference
samples.
A SummarizedExperiment object containing at least
the reference samples for each batch in sce.
Matrix with baseline-subtracted abundances.
sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
package = "einprot"))
## Introduce artificial batch column
sce$batch <- rep(c("B1", "B2", "B3"), 3)
SummarizedExperiment::colData(sce)
#> DataFrame with 9 rows and 5 columns
#> sample group nNA pNA batch
#> <character> <character> <numeric> <numeric> <character>
#> Adnp_IP04 Adnp_IP04 Adnp 54 23.3766 B1
#> Adnp_IP05 Adnp_IP05 Adnp 41 17.7489 B2
#> Adnp_IP06 Adnp_IP06 Adnp 50 21.6450 B3
#> Chd4BF_IP07 Chd4BF_IP0... Chd4BF 29 12.5541 B1
#> Chd4BF_IP08 Chd4BF_IP0... Chd4BF 9 3.8961 B2
#> Chd4BF_IP09 Chd4BF_IP0... Chd4BF 38 16.4502 B3
#> RBC_ctrl_IP01 RBC_ctrl_I... RBC_ctrl 107 46.3203 B1
#> RBC_ctrl_IP02 RBC_ctrl_I... RBC_ctrl 104 45.0216 B2
#> RBC_ctrl_IP03 RBC_ctrl_I... RBC_ctrl 105 45.4545 B3
mat <- getMatSubtractedBaseline(sce, assayName = "log2_LFQ.intensity",
baselineGroup = "RBC_ctrl",
sceFull = sce)
## After the subtraction, the baseline samples are equalized across the
## different batches
head(mat)
#> Adnp_IP04 Adnp_IP05 Adnp_IP06 Chd4BF_IP07 Chd4BF_IP08 Chd4BF_IP09
#> Dhx9 24.18116 26.01048 24.73828 21.76343 23.27155 23.00110
#> Zmynd8 19.28486 15.91157 19.32624 22.74219 22.65350 22.62484
#> Zmym4 26.34049 24.01694 28.46780 23.83731 29.34545 23.59778
#> Rlf 24.30727 21.89682 24.68757 19.31752 26.86482 20.61771
#> Zfp600 23.04364 22.97297 23.89353 22.92493 25.23942 23.68068
#> Rpl32 17.29039 25.15371 22.00468 18.73304 24.39710 22.46536
#> RBC_ctrl_IP01 RBC_ctrl_IP02 RBC_ctrl_IP03
#> Dhx9 15.95417 15.95417 15.95417
#> Zmynd8 16.06443 16.06443 16.06443
#> Zmym4 16.43556 16.43556 16.43556
#> Rlf 16.45595 16.45595 16.45595
#> Zfp600 22.24619 22.24619 22.24619
#> Rpl32 18.04745 18.04745 18.04745