An object of class
Biobase::ExpressionSet
containing transcriptomics data for differential analysis and (once
transformed to log\(_2\) counts per million reads) WGCNA.
TRNSCRPT_EXPObject of class
Biobase::ExpressionSet with
16404 features and 48 samples.
The original 32883 transcripts were filtered with
filterByExpr using group =
TRNSCRPT_EXP[["exp_group"]]. Then, library sizes were TMM normalized
with calcNormFactors. Two outlier samples (90423017005
and 90410017005) were removed before variables pct_globin,
rin, pct_umi_dup, and median_5_3_bias were
mean-imputed, centered, and scaled.
See OUTLIERS for sample outlier
information.
See FEATURE_TO_GENE for details of
feature-to-gene mapping.
library(Biobase)
TRNSCRPT_EXP # summary
#> ExpressionSet (storageMode: lockedEnvironment)
#> assayData: 16404 features, 48 samples
#> element names: exprs
#> protocolData: none
#> phenoData
#> sampleNames: 90245017005 90248017005 ... 90227017005 (48 total)
#> varLabels: pid bid ... median_5_3_bias (11 total)
#> varMetadata: labelDescription
#> featureData
#> featureNames: ENSRNOG00000000001 ENSRNOG00000000007 ...
#> ENSRNOG00000062306 (16404 total)
#> fvarLabels: feature_ID gene_symbol entrez_gene
#> fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> Annotation:
exprs(TRNSCRPT_EXP)[1:10, 1:5] # assayData (first 10 rows and 5 columns)
#> 90245017005 90248017005 90252017005 90265017005 90266017005
#> ENSRNOG00000000001 28 14 23 28 35
#> ENSRNOG00000000007 5 12 7 7 1
#> ENSRNOG00000000008 110 53 114 88 87
#> ENSRNOG00000000010 54 17 3 7 14
#> ENSRNOG00000000012 106 153 158 103 209
#> ENSRNOG00000000017 34 54 61 37 64
#> ENSRNOG00000000021 721 321 326 367 436
#> ENSRNOG00000000024 493 773 674 644 847
#> ENSRNOG00000000033 512 323 403 377 411
#> ENSRNOG00000000034 490 279 425 301 447
head(fData(TRNSCRPT_EXP)) # featureData
#> feature_ID gene_symbol entrez_gene
#> ENSRNOG00000000001 ENSRNOG00000000001 AABR07013255.1 <NA>
#> ENSRNOG00000000007 ENSRNOG00000000007 Gad1 24379
#> ENSRNOG00000000008 ENSRNOG00000000008 Alx4 296511
#> ENSRNOG00000000010 ENSRNOG00000000010 Cbln1 498922
#> ENSRNOG00000000012 ENSRNOG00000000012 Tcf15 296272
#> ENSRNOG00000000017 ENSRNOG00000000017 Steap1 297738
head(pData(TRNSCRPT_EXP)) # phenoData
#> pid bid labelid viallabel sex timepoint exp_group
#> 90245017005 10043527 90245 4.458696e-313 90245017005 Female SED F_SED
#> 90248017005 10043950 90248 4.458844e-313 90248017005 Female SED F_SED
#> 90252017005 10044337 90252 4.459042e-313 90252017005 Female SED F_SED
#> 90265017005 10046119 90265 4.459684e-313 90265017005 Female SED F_SED
#> 90266017005 10046380 90266 4.459734e-313 90266017005 Female SED F_SED
#> 90560017005 10700102 90560 4.474259e-313 90560017005 Female 1W F_1W
#> rin pct_globin pct_umi_dup median_5_3_bias
#> 90245017005 0.1534937 -0.3394055 3.1014362 0.98444319
#> 90248017005 -2.0568155 1.0182164 0.3599009 -2.07005015
#> 90252017005 -2.5479953 0.3394055 -0.0376748 -1.03230562
#> 90265017005 -1.5656357 -0.3394055 -0.5626291 0.53410122
#> 90266017005 -0.3376861 0.3394055 -0.4034058 -0.05982804
#> 90560017005 -2.3024054 1.6970274 -0.2760272 -1.97214972