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missing additional visits in GSE data

When downloading GSE data, often I encounter that the authors refer to additional visits in the data description, yet, they are not found in the data. For example, the following study. They mention ...
Kozolovska's user avatar
1 vote
0 answers
29 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 ...
Riesz98's user avatar
  • 41
1 vote
1 answer
63 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 ...
Zebra Fish's user avatar
2 votes
0 answers
49 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 ...
accibio's user avatar
  • 145
1 vote
1 answer
182 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 ...
accibio's user avatar
  • 145
1 vote
1 answer
318 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 ...
Angus Campbell's user avatar
0 votes
1 answer
659 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 ...
chickenNinja123's user avatar
0 votes
1 answer
139 views

Error downloading GSE dataset

I've installed GEOquery with install.packages("BiocManager") BiocManager::install("GEOquery") library(GEOquery) then I ran the command ...
Jaemin Kim's user avatar
1 vote
1 answer
162 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). ...
Angus Campbell's user avatar
0 votes
1 answer
75 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- ...
Vishal Kumar Sahu's user avatar
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: ...
An Ignorant Wanderer's user avatar
2 votes
0 answers
273 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 ...
Sylvia Rodriguez's user avatar
3 votes
3 answers
7k 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 ...
Diana at Duke's user avatar
1 vote
0 answers
108 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 ...
Anjan Bharadwaj's user avatar
1 vote
1 answer
942 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 ...
Qiran's user avatar
  • 11
1 vote
1 answer
749 views

GEOquery errors due to list input

I want to extract the expression matrix from the GSE object in GEOquery. ...
Subinoy Biswas's user avatar
0 votes
2 answers
108 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 ...
Natasha's user avatar
  • 125
1 vote
1 answer
78 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 ...
Natasha's user avatar
  • 125
1 vote
1 answer
1k 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 ...
Eman Ismail's user avatar
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 ...
J. Doe's user avatar
  • 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. ...
panbar's user avatar
  • 81