Questions tagged [geo]

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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 ...
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43 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 ...
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15 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 ...
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27 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 ...
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2answers
39 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&...
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37 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 ...
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2answers
126 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?
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57 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 ...
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1answer
595 views

GEOquery errors due to list input

I want to extract the expression matrix from the GSE object in GEOquery. ...
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1answer
59 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 ...