Retrieve datasets by their identifiers
get_datasets_by_ids(
datasets = NA_character_,
filter = NA_character_,
taxa = NA_character_,
uris = NA_character_,
offset = 0L,
limit = 20L,
sort = "+id",
raw = getOption("gemma.raw", FALSE),
memoised = getOption("gemma.memoised", FALSE),
file = getOption("gemma.file", NA_character_),
overwrite = getOption("gemma.overwrite", FALSE)
)Numerical dataset identifiers or dataset short names. If not specified, all datasets will be returned instead
Filter results by matching expression. Use filter_properties
function to get a list of all available parameters. These properties can be
combined using "and" "or" clauses and may contain common operators such as "=", "<" or "in".
(e.g. "taxon.commonName = human", "taxon.commonName in (human,mouse), "id < 1000")
A vector of taxon common names (e.g. human, mouse, rat). Providing multiple
species will return results for all species. These are appended
to the filter and equivalent to filtering for taxon.commonName property
A vector of ontology term URIs. Providing multiple terms will
return results containing any of the terms and their children. These are
appended to the filter and equivalent to filtering for allCharacteristics.valueUri
The offset of the first retrieved result.
Defaults to 20. Limits the result to specified amount
of objects. Has a maximum value of 100. Use together with offset and
the totalElements attribute in the output to
compile all data if needed.
Order results by the given property and direction. The '+' sign indicate ascending order whereas the '-' indicate descending.
TRUE to receive results as-is from Gemma, or FALSE to enable
parsing. Raw results usually contain additional fields and flags that are
omitted in the parsed results.
Whether or not to save to cache for future calls with the
same inputs and use the result saved in cache if a result is already saved.
Doing options(gemma.memoised = TRUE) will ensure that the cache is always
used. Use forget_gemma_memoised to clear the cache.
The name of a file to save the results to, or NULL to not write
results to a file. If raw == TRUE, the output will be the raw endpoint from the
API, likely a JSON or a gzip file. Otherwise, it will be a RDS file.
Whether or not to overwrite if a file exists at the specified filename.
A data table with information about the queried dataset(s). A list if
raw = TRUE. Returns an empty list if no datasets matched.
The fields of the output data.table are:
experiment.shortName: Shortname given to the dataset within Gemma. Often corresponds to accession ID
experiment.name: Full title of the dataset
experiment.ID: Internal ID of the dataset.
experiment.description: Description of the dataset
experiment.troubled: Did an automatic process within gemma or a curator mark the dataset as "troubled"
experiment.accession: Accession ID of the dataset in the external database it was taken from
experiment.database: The name of the database where the dataset was taken from
experiment.URI: URI of the original database
experiment.sampleCount: Number of samples in the dataset
experiment.batchEffectText: A text field describing whether the dataset has batch effects
experiment.batchCorrected: Whether batch correction has been performed on the dataset.
experiment.batchConfound: 0 if batch info isn't available, -1 if batch counfoud is detected, 1 if batch information is available and no batch confound found
experiment.batchEffect: -1 if batch p value < 0.0001, 1 if batch p value > 0.1, 0 if otherwise and when there is no batch information is available or when the data is confounded with batches.
experiment.rawData: -1 if no raw data available, 1 if raw data was available. When available, Gemma reprocesses raw data to get expression values and batches
geeq.qScore: Data quality score given to the dataset by Gemma.
geeq.sScore: Suitability score given to the dataset by Gemma. Refers to factors like batches, platforms and other aspects of experimental design
taxon.name: Name of the species
taxon.scientific: Scientific name for the taxon
taxon.ID: Internal identifier given to the species by Gemma
taxon.NCBI: NCBI ID of the taxon
taxon.database.name: Underlying database used in Gemma for the taxon
taxon.database.ID: ID of the underyling database used in Gemma for the taxon
get_datasets_by_ids("GSE2018")
#> experiment.shortName experiment.name experiment.ID
#> <char> <char> <int>
#> 1: GSE2018 Human Lung Transplant - BAL 1
#> experiment.description
#> <char>
#> 1: Bronchoalveolar lavage samples collected from lung transplant recipients. Numeric portion of sample name is an arbitrary patient ID and AxBx number indicates the perivascular (A) and bronchiolar (B) scores from biopsies collected on the same day as the BAL fluid was collected. Several patients have more than one sample in this series and can be determined by patient number followed by a lower case letter. Acute rejection state is determined by the combined A and B score - specifically, a combined AB score of 2 or greater is considered an acute rejection.
#> experiment.troubled experiment.accession experiment.database
#> <lgcl> <char> <char>
#> 1: FALSE GSE2018 GEO
#> experiment.URI
#> <char>
#> 1: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2018
#> experiment.sampleCount experiment.lastUpdated experiment.batchEffectText
#> <int> <POSc> <char>
#> 1: 34 2024-02-10 08:31:41 NO_BATCH_EFFECT_SUCCESS
#> experiment.batchCorrected experiment.batchConfound experiment.batchEffect
#> <lgcl> <num> <num>
#> 1: FALSE 1 1
#> experiment.rawData geeq.qScore geeq.sScore taxon.name taxon.scientific
#> <num> <num> <num> <char> <char>
#> 1: 1 0.9976341 0.875 human Homo sapiens
#> taxon.ID taxon.NCBI taxon.database.name taxon.database.ID
#> <int> <int> <char> <int>
#> 1: 1 9606 hg38 87
get_datasets_by_ids(c("GSE2018", "GSE2872"))
#> experiment.shortName experiment.name experiment.ID
#> <char> <char> <int>
#> 1: GSE2018 Human Lung Transplant - BAL 1
#> 2: GSE2872 d'mel-affy-rat-168311 2
#> experiment.description
#> <char>
#> 1: Bronchoalveolar lavage samples collected from lung transplant recipients. Numeric portion of sample name is an arbitrary patient ID and AxBx number indicates the perivascular (A) and bronchiolar (B) scores from biopsies collected on the same day as the BAL fluid was collected. Several patients have more than one sample in this series and can be determined by patient number followed by a lower case letter. Acute rejection state is determined by the combined A and B score - specifically, a combined AB score of 2 or greater is considered an acute rejection.
#> 2: Neurological diseases disrupt the quality of the lives of patients and often lead to their death prematurely. A common feature of most neurological diseases is the degeneration of neurons, which results from an inappropriate activation of apoptosis. Drugs that inhibit neuronal apoptosis could thus be candidates for therapeutic intervention in neurodegenerative disorders. We have identified (and recently reported) a chemical called GW5074 that inhibits apoptosis in a variety of cell culture paradigms of neuronal apoptosis. Additionally, we have found that GW5074 reduces neurodegeneration and improves behavioral outcome in a mouse model of Huntington's disease. Although GW5074 is a c-Raf inhibitor, we know very little about the molecular mechanisms underlying its neuroprotective action. Identifying genes that are regulated by GW5074 in neurons will shed insight into this issue. We believe that neuroprotection by GW5074 involves the regulation of several genes. Some of these genes are likely to be induced whereas the expression of other genes might be inhibited. The specific aim is to identify genes that are differentially expressed in neurons treated with GW5074. We believe that neuroprotection by GW5074 involves the regulation of several genes. Some of these genes are likely to be induced whereas the expression of other genes might be inhibited. Cultures of cerebellar granule neurons undergo apoptosis when switched from medium containing levated levels of potassium (high K+ or HK) to medium containing low potassium (LK). Although cell death begins at about 18 h, we have found that the by 6 h after LK treatment these neurons are irreversibly committed to cell death. We will treat cerebellar granule neuron cultures with LK medium (which induces them to undergo apoptosis) or with GW5074 (1 uM). We will extract RNA at two time-points after treatment: 3 h and 6 h. Analysis at the two different time-points will show us whether changes in expression of specific genes is transient or sustained or whether the changes occurs early or relatively late in the process. Neuronal cultures will be prepared from 1 week old Wistar rats. The cultures will be maintained in culture for 1 week before treatment. Following treatment the cells will be lysed and total RNA isolated. The RNA will be stored at -80oC and shipped to the microarray facility for analysis. The experiment will be done in triplicate. Thus, for each time-point (3 or 6h treatment) we will be hope to provide 3 sets of samples (each set coming from a different culture preparation and containing lysates from cells treated with LK or GW5074). Having samples from 3 independent cultures will mitigate any expression differences resulting from subtle variations in culture quality or in the preparation or quality of RNA.\nDate GSE2872 Last Updated: Jul 06 2005\nContributors: S R D'Mello\nIncludes GDS1837.\n Update date: Jun 09 2006.\n Dataset description GDS1837: Analysis of cultured cerebellar granule neurons in low potassium medium 3 and 6 hours following treatment with the c-Raf inhibitor GW5074. GW5074 blocks low potassium induced cell death. Results provide insight into the neuroprotective action of GW5074.
#> experiment.troubled experiment.accession experiment.database
#> <lgcl> <char> <char>
#> 1: FALSE GSE2018 GEO
#> 2: FALSE GSE2872 GEO
#> experiment.URI
#> <char>
#> 1: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2018
#> 2: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2872
#> experiment.sampleCount experiment.lastUpdated experiment.batchEffectText
#> <int> <POSc> <char>
#> 1: 34 2024-02-10 08:31:41 NO_BATCH_EFFECT_SUCCESS
#> 2: 12 2024-01-02 18:57:36 SINGLE_BATCH_SUCCESS
#> experiment.batchCorrected experiment.batchConfound experiment.batchEffect
#> <lgcl> <num> <num>
#> 1: FALSE 1 1
#> 2: FALSE 1 1
#> experiment.rawData geeq.qScore geeq.sScore taxon.name taxon.scientific
#> <num> <num> <num> <char> <char>
#> 1: 1 0.9976341 0.875 human Homo sapiens
#> 2: 1 0.8552303 0.500 rat Rattus norvegicus
#> taxon.ID taxon.NCBI taxon.database.name taxon.database.ID
#> <int> <int> <char> <int>
#> 1: 1 9606 hg38 87
#> 2: 3 10116 rn6 86