Questions tagged [geoquery]
The geoquery tag has no usage guidance.
20
questions
1
vote
0
answers
26
views
David tool online not converting most genes
I'm using DAVID tool online, in order to perform functional annotation chart. I extracted the most relevant genes from a dataset (GSE73304), but have the problem that DAVID is not able to understand ...
- 41
1
vote
1
answer
57
views
How do you extract the full list of files in a GEO archive?
I am new to use of GEO and having trouble figuring out a straightforward way to grab the names of the files, (through programmable handles like GEOparse or otherwise) that is the entire and complete ...
- 323
2
votes
0
answers
35
views
illuminaHumanv2.db returning NA for all Illumina probe ID to gene symbol conversion [closed]
This question has been cross-posted on Biostars but has not received any answers yet, so I'm posting it here. I'll update here if it gets answered there.
I have downloaded a miRNA expression dataset ...
- 145
1
vote
1
answer
126
views
DESeq2 throwing error while normalizing raw microarray expression data due to presence of negative values
This question was also asked on Biostars
I am trying to download and analyze a miRNA expression dataset from NCBI GEO (GSE25631). I specifically want non-normalized ...
- 145
1
vote
1
answer
195
views
Gene symbol list for all protein coding genes in mice
How can I get a csv or a list of the gene symbol names for all the protein coding genes in mice? I have RNA sequencing data and I'm not interested in the non-coding stuff. I'm worried it could mess ...
- 376
0
votes
1
answer
532
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 ...
- 103
0
votes
1
answer
116
views
Error downloading GSE dataset
I've installed GEOquery with
install.packages("BiocManager")
BiocManager::install("GEOquery")
library(GEOquery)
then I ran the command
...
- 11
1
vote
1
answer
146
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).
...
- 376
0
votes
1
answer
66
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-
...
0
votes
1
answer
45
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
votes
0
answers
257
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 ...
- 257
3
votes
3
answers
6k
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 ...
1
vote
0
answers
103
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 ...
- 111
1
vote
1
answer
889
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 ...
- 11
1
vote
1
answer
742
views
GEOquery errors due to list input
I want to extract the expression matrix from the GSE object in GEOquery.
...
0
votes
2
answers
104
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 ...
- 125
1
vote
1
answer
76
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 ...
- 125
1
vote
1
answer
973
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
...
- 35
2
votes
1
answer
76
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 ...
- 575
8
votes
1
answer
7k
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.
...
- 81