Questions tagged [geo]
18
questions
2
votes
1
answer
34
views
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 ...
- 73
1
vote
1
answer
59
views
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 ...
- 41
2
votes
1
answer
40
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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 ...
- 41
1
vote
1
answer
57
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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
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 ...
- 4,693
1
vote
1
answer
126
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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
194
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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
3
votes
1
answer
39
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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, ...
- 339
1
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1
answer
179
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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 ...
- 470
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
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 ...
0
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1
answer
39
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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 ...
0
votes
2
answers
119
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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&...
- 63
0
votes
0
answers
74
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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 ...
1
vote
2
answers
292
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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?
1
vote
0
answers
103
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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
742
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GEOquery errors due to list input
I want to extract the expression matrix from the GSE object in GEOquery.
...
2
votes
1
answer
165
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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 ...
- 2,538