Questions tagged [geo]

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How to find the file names referred to in the R script produced by GEO2R in GEO Accession

I am new to both coding and GEO so this may be a silly question. I need the raw_counts data set for the GEO data set I am using but data in the downloads box is not the raw_counts. How would I be able ...
Sabrina's user avatar
  • 73
1 vote
1 answer
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Read methylation data from tar files on GEO (GSE73303)

I'm trying to analyise methylation data using GEO, in order to conduct a multi-omics analysis. The SubSeries I am referring to is GSE73303. Unfortunately, the code used to inspect it produces empty ...
Riesz98's user avatar
  • 41
2 votes
1 answer
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GEO Methylation dataset "GSE73303" shows 0 features

I'm working for a project using GEO, in order to analyze some gene expression data. The SuperSeries I am referring to is GSE73304, but I found some problems working on the SubSeries GSE73303. I ...
Riesz98's user avatar
  • 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 ...
Zebra Fish's user avatar
0 votes
0 answers
31 views

Get BioProject code of a GEO dataset

In publications the GEO code is usually shared and not the BioProject/study code. I want to get the BioProject/Study Accession code of a GEO dataset (to later download the data from ENA). I know that ...
llrs's user avatar
  • 4,693
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 ...
accibio's user avatar
  • 145
1 vote
1 answer
194 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
3 votes
1 answer
39 views

Is there a way I can combine geological data with population genetics data?

So I have ran SAMOVA and made calculations regarding haplotype diversity and nucleotide diversity of several populations. I have also made raster data regarding geographical data like slope, ...
Nickmofoe's user avatar
  • 339
1 vote
1 answer
179 views

Convert SNP data from GEO into PED and MAP files?

I can easily grab SNP-Chip data from NCBI's GEO database for a given Illumina SNP-Chip array, e.g. from here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52147 GEO provides data as SOFT ...
Dan Bolser's user avatar
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 ...
chickenNinja123's user avatar
1 vote
1 answer
75 views

Difference in Calculation through GEO2R and difference in Article

Here is microarray analysis where author uses GSE50632 series on an Agilent microarray GPL17660 platform with 4 eligible samples which I guess are GSM1224991, GSM1224992, GSM1224993 and GSM1224994 ...
Vishal Kumar Sahu's user avatar
0 votes
1 answer
39 views

multi--platform GEO analysis based in expression of single gene

This question has also been asked on Biostars I have a challenge in analyzing GSE34941( It has 4 platforms) according to the expression of a specific gene in R. First, which is the best way to group ...
amir navidi's user avatar
0 votes
2 answers
119 views

Getting Unique Identifier List for GEO Datasets NCBI

AIM: Download "Unique Identifier List" for the following query from GEO DataSets. Query: ("Expression profiling by high throughput sequencing"[DataSet Type] AND ("Homo sapiens&...
Pawan Verma's user avatar
0 votes
0 answers
74 views

Trying to retrieve sra data using sra explorer

I am trying to use the SRA explorer tool to download data from ENA. Whatever geo accession number I give it however, it will return no results. It only seems to return results for the suggestions it ...
An Ignorant Wanderer's user avatar
1 vote
2 answers
292 views

How to tell if library generation for RNA-seq experiments are stranded vs not stranded

I would like to use RNA-seq data from the NIH GEO database. How can I tell if library generation for the RNA-seq experiments are stranded vs not stranded?
An Ignorant Wanderer's user avatar
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 ...
Anjan Bharadwaj's user avatar
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. ...
Subinoy Biswas's user avatar
2 votes
1 answer
165 views

Article GEO gives counts that are not integers. Should UMI counts be integers?

I thought that UMI counts are always integers, but when I opened several datasets provided by GEO I got confused because in some ...
Nikita Vlasenko's user avatar