An object of class
Biobase::ExpressionSet
containing median-MAD-normalized log\(_2\)-transformed protein
phosphorylation data.
PHOSPHO_EXPObject of class
Biobase::ExpressionSet with
30304 features and 60 samples.
RAT_TO_HUMAN_PHOSPHO for
details of mapping between rat and human phosphorylation sites.
See FEATURE_TO_GENE for details of
feature-to-gene mapping.
library(Biobase)
PHOSPHO_EXP # summary
#> ExpressionSet (storageMode: lockedEnvironment)
#> assayData: 30304 features, 60 samples
#> element names: exprs
#> protocolData: none
#> phenoData
#> sampleNames: 90222017006 90258017006 ... 90237017006 (60 total)
#> varLabels: pid bid ... exp_group (7 total)
#> varMetadata: labelDescription
#> featureData
#> featureNames: NP_001001504.1_S448s NP_001001512.2_S228s ...
#> XP_345868.4_T633t (30304 total)
#> fvarLabels: feature_ID gene_symbol ... human_site (7 total)
#> fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> Annotation:
exprs(PHOSPHO_EXP)[1:10, 1:5] # assayData (first 10 rows and 5 columns)
#> 90222017006 90258017006 90441017006 90266017006
#> NP_001001504.1_S448s NA NA NA NA
#> NP_001001512.2_S228s 0.1112 -0.0098 0.1768 -0.2122
#> NP_001001801.1_S30s NA NA NA NA
#> NP_001002016.2_S12s -0.0295 0.0111 -0.1142 -0.1185
#> NP_001002016.2_S143s NA NA NA NA
#> NP_001002016.2_S153s -0.5996 0.3427 -0.3792 0.1080
#> NP_001002016.2_S17s -0.2917 0.2004 -0.7424 0.1419
#> NP_001002016.2_S18s -0.0802 0.1502 -0.1014 0.0237
#> NP_001002016.2_S212s NA NA NA NA
#> NP_001002016.2_S22s 0.1182 -0.1563 0.4189 -0.1975
#> 90421017006
#> NP_001001504.1_S448s NA
#> NP_001001512.2_S228s 0.2223
#> NP_001001801.1_S30s NA
#> NP_001002016.2_S12s 0.0288
#> NP_001002016.2_S143s NA
#> NP_001002016.2_S153s -0.4339
#> NP_001002016.2_S17s -0.4537
#> NP_001002016.2_S18s 0.0077
#> NP_001002016.2_S212s NA
#> NP_001002016.2_S22s 0.1365
head(fData(PHOSPHO_EXP)) # featureData
#> feature_ID gene_symbol entrez_gene site
#> NP_001001504.1_S448s NP_001001504.1_S448s Gtf2ird1 246770 S448
#> NP_001001512.2_S228s NP_001001512.2_S228s Gtf2i 353256 S228
#> NP_001001801.1_S30s NP_001001801.1_S30s Akap7 361458 S30
#> NP_001002016.2_S12s NP_001002016.2_S12s Lmna 60374 S12
#> NP_001002016.2_S143s NP_001002016.2_S143s Lmna 60374 S143
#> NP_001002016.2_S153s NP_001002016.2_S153s Lmna 60374 S153
#> human_feature_ID human_uniprot human_site
#> NP_001001504.1_S448s Q9UHL9_S448s Q9UHL9 S448
#> NP_001001512.2_S228s <NA> <NA> <NA>
#> NP_001001801.1_S30s <NA> <NA> <NA>
#> NP_001002016.2_S12s P02545_S12s P02545 S12
#> NP_001002016.2_S143s P02545_S143s P02545 S143
#> NP_001002016.2_S153s P02545_S153s P02545 S153
head(pData(PHOSPHO_EXP)) # phenoData
#> pid bid labelid viallabel sex timepoint exp_group
#> 90222017006 10025626 90222 4.457560e-313 90222017006 Male 8W M_8W
#> 90258017006 10045228 90258 4.459338e-313 90258017006 Female 8W F_8W
#> 90441017006 10502300 90441 4.468380e-313 90441017006 Male 2W M_2W
#> 90266017006 10046380 90266 4.459734e-313 90266017006 Female SED F_SED
#> 90421017006 10417702 90421 4.467392e-313 90421017006 Male 1W M_1W
#> 90410017006 10335064 90410 4.466848e-313 90410017006 Female 4W F_4W