2024-04-02
The data set can be found at GEO gse24243.
Using package ArrayExpress.
Let us see the class.
datosexperimento = new('MIAME',name='Flowers MT, Scheisser K, Dawson JA,
Kendziorski C, Ntambi JM',
lab='James Ntambi',
contact ='mtflowers@wisc.edu',
title = 'Metabolic changes in skin caused by Scd1 deficiency: a focus on
retinol metabolism.',
abstract = 'To help elucidate the metabolic changes in the skin that
contribute to the obesity resistance and skin pathology in mice lacking Scd1, we performed microarray analysis of skin gene expression in male skin Scd1 knockout (SKO) and Scd1 flox/flox control (Lox) mice fed a standard rodent diet. We identified an extraordinary number of differentially expressed genes that support the previously documented histological observations of sebocyte atrophy, inflammation and epidermal hyperplasia in SKO mice. Additionally, transcript levels were reduced in skin of SKO mice for genes involved in fatty acid synthesis, elongation and desaturation, which may be attributed to decreased abundance of key transcription factors including SREBP1c, ChREBP and LXR. Conversely, genes involved in cholesterol synthesis were increased, suggesting an imbalance between skin fatty acid and cholesterol synthesis. Unexpectedly, we observed a robust elevation in skin retinol, retinoic acid and retinoic acid-induced genes in SKO mice. These results highlight the importance of monounsaturated fatty acid synthesis for maintaining retinol homeostasis and point to disturbed retinol metabolism as a novel contributor to the Scd1 deficiency-induced skin pathology. We analyzed dorsal skin gene expression in non-fasted 8-9 week old male skin Scd1 knockout (SKO) mice (n=3) and Scd1flox/flox (Lox) control mice (n=3)on a C57BL/6J background using Affymetrix 430 2.0 microarrays.',
url = 'https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24243/'
)
experimentData(geod24243) = datosexperimento
Let us simplify the problem and we are going to consider just the correspondences with ENTREZID
.
We have multiple correspondences.
names(b)
we have more than one gene.data.frame
.ENTREZID
identifier has a unique PROBEID
identifier.ENTREZID
.PROBEID
with ENTREZID
and ENSEMBL
.Let us see the dimension of a
.
The ENSEMBL
identifiers are not unique.