BatchQC 2.2.0
This data set is from protein expression data captured for 39 proteins. It has two batches and two conditions corresponding to case and control.
library(BatchQC)
data(protein_data)
data(protein_sample_info)
se_object <- BatchQC::summarized_experiment(protein_data, protein_sample_info)This data set is from signature data captured when activating different growth pathway genes in human mammary epithelial cells (GEO accession: GSE73628). This data consists of three batches and ten different conditions corresponding to control and nine different pathways
data(signature_data)
data(batch_indicator)
se_object <- BatchQC::summarized_experiment(signature_data, batch_indicator)This data set is from bladder cancer data. This dataset has 57 bladder samples with 5 batches and 3 covariate levels (cancer, biopsy, control). Batch 1 contains only cancer, 2 has cancer and controls, 3 has only controls, 4 contains only biopsy, and 5 contains cancer and biopsy. This data set is from the bladderbatch package which must be installed to use this data example set (Leek JT (2023). bladderbatch: Bladder gene expression data illustrating batch effects. R package version 1.38.0).
if (!requireNamespace("bladderbatch", quietly = TRUE))
BiocManager::install("bladderbatch")
se_object <- BatchQC::bladder_data_upload()## R version 4.4.1 (2024-06-14)
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## time zone: America/New_York
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
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## other attached packages:
## [1] BatchQC_2.2.0 BiocStyle_2.34.0
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