Questions tagged [geoquery]

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40 views

Why am I getting empty expression data from GEO?

I am trying to analyze the scRNAseq data from this study. In their Method section they write: The accession number for the RNA and DNaseq data reported in this paper is GEO: GSE116237. When I go ...
-1
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1answer
47 views

Error downloading GSE dataset

I've installed GEOquery with >install.packages("BiocManager") >BiocManager::install("GEOquery") >library(GEOquery). then I ran the ...
1
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1answer
35 views

Calling GEOquerry error while loading the library

Note: this question has also been asked on Biostars I started getting a strange error when trying to load GEOquerry with library(GEOquerry). ...
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1answer
11 views

How is the t-statistic value calculated in GEO2R or Bioconductor?

I was trying to calculate t-statistics using Python's scipy and numpy as np- ...
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1answer
38 views

How can I restrict the search space when querying GEO?

I am using the following command to retrieve GEO Datasets entries for daf-2 c. elegans that have as their experiment type High Throughpout sequencing: ...
2
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0answers
93 views

How can I collapse probes to single value per gene using GEOquery?

I have extracted microarray gene expression data from GEO using the GEOquery package in R. There are multiple probes per gene. Is there a way to select the best ...
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3answers
2k views

How do I pull singe cell RNA sequencing data from GEO database?

I am new to R and computational biology. I am trying to look through a published data set to check for gene expression for my own project. I am having trouble finding materials to teach me how to ...
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0answers
56 views

Mapping GPL Platform Number to Microarray Name

I am trying to download a dataset from GEO using the GEOquery R package. Using this package, I can retrieve the GPL platform number(s) for the dataset, and I hope to use a CDF file from BrainArray on ...
1
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1answer
422 views

Extracting expression data in r from GEO and got a S4 object

I want to open the expression data GSE9838 dataset from GEO using GEOquery R package. gset <- getGEO(filename="GSE9838_family.soft.gz") The result of this ...
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1answer
579 views

GEOquery errors due to list input

I want to extract the expression matrix from the GSE object in GEOquery. ...
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2answers
86 views

Comparing the gene expression data

I'm trying to compare the gene expression data reported in the studies documented in GEO for a specific gene expressed in a tissue of my interest in Homo sapiens. I compared the values reported in 4 ...
1
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1answer
66 views

Parsing gene expression value for a list of genes from GEO

I am looking for the gene expression data in GEO GSE15543 with the following keywords, (Pancreatic Beta Cells) AND "Homo sapiens"[porgn:__txid9606] I ...
1
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1answer
537 views

Get Gene Expression Matrix from GEOquery

I am trying to get gene expression matrix for a list of genes I have for my list: Gene ID, Gene Symbol How can I get for each gene corresponding expression as array?? I suppose that I will have ...
2
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1answer
67 views

coexnet package for network co-expression analysis, is looking for a filelist.txt that doesn't exist

On my way to create a co-expression matrix for a microarray experiment, using the coexnet package I had to use a function called ...
8
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1answer
6k views

Extracting expression data from GSE dataset downloaded from GEO

I have downloaded GSE16146 dataset from GEO using GEOquery R package. I would like to extract "Data table" from downloaded GSE16146. ...