Commit 63b80f95 authored by Leon-Charles Tranchevent's avatar Leon-Charles Tranchevent
Browse files

Revision of the limma strategy with respect to the potential experimental batches.

parent d9be7f6f
......@@ -109,6 +109,7 @@ for (i in seq_len(length(config$datasets))) {
.funs = collapser) %>%
dplyr::ungroup()
gene_annots <- gene_annots[order(match(gene_annots$PROBEID, rownames(exp_eset))), ]
# Just in case, for RNA-seq data, we use the following alternative to the above statment.
# This is only placed there for information since it was not used for miicroarray data.
# The current solution is equivalent.
......@@ -180,7 +181,7 @@ for (i in seq_len(length(config$datasets))) {
correct_for_batch = dataset$has_batches,
cofactor_name = "Tissue",
block_key = "Patient",
run_topconfects = TRUE,
run_topconfects = FALSE,
output_data_dir = output_data_dir,
file_prefix = dataset_name,
file_suffix = vsn$name,
......@@ -193,7 +194,7 @@ for (i in seq_len(length(config$datasets))) {
fit <- ArrayUtils::run_limma(pheno_data, exp_eset, limma_parameters,
correct_for_age = age_correct,
correct_for_batch = dataset$has_batches,
run_topconfects = TRUE,
run_topconfects = FALSE,
output_data_dir = output_data_dir,
file_prefix = dataset_name,
file_suffix = vsn$name,
......
......@@ -3,13 +3,13 @@ GSE20141 Affymetrix HGU133Plus2 D FALSE TRUE FALSE TRUE DA
GSE20163 Affymetrix HGU133A D FALSE FALSE FALSE TRUE SN
GSE20164 Affymetrix HGU133A DG FALSE TRUE FALSE TRUE SN
GSE20292 Affymetrix HGU133A DG FALSE FALSE FALSE TRUE SN
GSE7307 Affymetrix HGU133Plus2 DG FALSE FALSE FALSE FALSE SN
GSE7307 Affymetrix HGU133Plus2 DG FALSE TRUE FALSE FALSE SN
GSE7621 Affymetrix HGU133Plus2 DG FALSE FALSE FALSE FALSE SN
GSE8397 Affymetrix HGU133A DG TRUE TRUE FALSE TRUE SN
GSE8397 Affymetrix HGU133A DG TRUE FALSE FALSE TRUE SN
Simunovic Affymetrix HGU133A DG FALSE TRUE FALSE TRUE DA
GSE24378 Affymetrix U133_X3P D FALSE TRUE FALSE TRUE DA
GSE20333 Affymetrix HG-Focus DG FALSE FALSE FALSE TRUE SN
Moreira Agilent G4112F DG FALSE FALSE FALSE TRUE SN
GSE20159 Illumina HumanV3 DG FALSE FALSE FALSE TRUE SN
GSE20159 Illumina HumanV3 DG FALSE TRUE FALSE TRUE SN
GSE26927 Illumina HumanV2 DGA FALSE FALSE TRUE TRUE SN
GSE49036 Affymetrix HGU133Plus2 DGA FALSE FALSE FALSE TRUE SN
\ No newline at end of file
......@@ -45,7 +45,7 @@ datasets:
array_type: HGU133Plus2
clinical_descriptors: DG
has_paired_samples: 'FALSE'
has_batches: 'FALSE'
has_batches: 'TRUE'
cleaning: 'FALSE'
has_age: 'FALSE'
tissue: SN
......@@ -65,7 +65,7 @@ datasets:
array_type: HGU133A
clinical_descriptors: DG
has_paired_samples: 'TRUE'
has_batches: 'TRUE'
has_batches: 'FALSE'
cleaning: 'FALSE'
has_age: 'TRUE'
tissue: SN
......@@ -115,7 +115,7 @@ datasets:
array_type: HumanV3
clinical_descriptors: DG
has_paired_samples: 'FALSE'
has_batches: 'FALSE'
has_batches: 'TRUE'
cleaning: 'FALSE'
has_age: 'TRUE'
tissue: SN
......
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