Tag: GEO2R

Introduction Chronic obstructive pulmonary disease (COPD) is a common chronic bronchitis disease characterized by persistent airflow limitation, which can be prevented and treated. COPD is the third leading cause of death in the world reported in 2020.1 With the progression of the disease, COPD will lead to respiratory failure, pulmonary…

Hello everyone, I’ve been having the same question for a while now. I’m also conducting my own analysis of differential expression on a microarray dataset in R. However, the data is different from the results obtained using GEO2R. Here’s my line of code: my_id <- “GSE80178” gse <- getGEO(my_id, GSEMatrix…

Analysis and results microarray data for research 0 Hello everyone, I am analyzing microarray and RNA-seq data in patients with diabetic foot ulcers for my research. I am an undergraduate student, and my group doesn’t have much experience with these types of analyses. I would like to receive some tips…

Large fold change when analyzing expression profiling from microarray 0 Hi, dear all. I am trying to analyze a expression profiling dataset from GEO, which was detected by Affymetrix microarray. Its data processing method was described as “The data were analyzed with Microarray Suite GCOS using Affymetrix default analysis settings…

Identifying common DEGs among multiple datasets 0 Hello everyone, I desperately need help here I have microarray and RNA-seq datasets on which I performed, individually, DEGs analysis using GEO2R Now I need to find the common DEGs between all these datasets using R software I am very lost and confused…

Geo2r rna seq analysis 0 Hello guys, I am relative new to rna seq data analysis. I would appreciate if anyone could ask my question.. To my understanding after u run rna seq analysis pipeline the information u get is whether the group under investigation ( lets call it disease…

Microarray DGE analysis 1 Hi, www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE30929 I have performed DGE analysis between WDLPS and DDLPS tumour samples in R and have the following results table. I ended up with the same results as the GEO2R. logFC AveExpr t P.Value adj.P.Val B 207175_at -5.7 8.8 -14 3.1e-25 7.0e-21 47 213706_at -3.5…

Tumor samples from patients Biopsies of primary breast tumors and breast tumors that had metastasized to the brain were obtained from patients with TNBC at the National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital of the Chinese Academy of Medical Sciences and Peking Union Medical College. Single-cell RNA sequencing…

Introduction As the leading cause of maternal mortality in early pregnancy, ectopic pregnancy (EP) is responsible for 4–10% of all pregnancy-related deaths,1 but drugs can only be used to treat early EP. However, significant differences in the effects on fertility between surgical treatment and medical treatment have been reported in…

Differential expression analysis We downloaded GSE125361 (n = 48) microarray data from the Gene Expression Omnibus (GEO) database, which included 45 myeloma samples and 3 controls, for expression analysis of IL5RA in cancer16. Additionally, we analyzed the expression of IL5RA in smoldering myeloma (SMM) patients who progressed to active MM (n = 10) and…

Introduction Among all common noncutaneous malignancies, bladder carcinoma (BC) is the fourth prevalent one in all patients from the United States, and a subset of BC can progress to a severe muscle invasive form, leading to distal metastasis to other organs, including liver, lung, bone and mediastinum (1). BC with…

Log2 FC Threshold 0 I’m using GEO2R in order to identify the DEGs, I set the significance level cut-off as 0.05. After the analysis, the log2 fc threshold was set automatically around 0.2 and 419 genes were defined as significant degs based on this threshold. My question is; can we…

Introduction Chronic obstructive pulmonary disease (COPD) is a common chronic respiratory condition that mostly occurs in middle-aged and elderly people. COPD manifests as a progressive airflow limitation associated with an abnormal lung inflammatory response.1 As a disease with high incidence, disability rate, long disease course, and multiple comorbidities, COPD has…

how to analyse methylation data from GEO? 0 how to analyse methylation data from GEO? can GEO2R be used for methylation data if it is available? please suggest Thanks methylation GEO GEO2R • 26 views • link updated 1 hour ago by Basti &starf; 1.4k • written 2 hours ago…

Introduction Multiple myeloma is a B-cell malignancy characterized by the malignant proliferation of clonal plasma cells in bone marrow,1 It is the second most common hematological malignancy after lymphoma.2 The age-standardised rate (ASR) of multiple myeloma incidence was 1·78 (95% UI 1·69-1·87) per 100 000 people globally and mortality was…

Introduction Stroke is one of the leading causes of death and disability worldwide, which causes substantial economic and social burdens.1 Ischemic stroke is caused by insufficient blood and oxygen supply to the brain,2 accounting for about 85% of the casualties of stroke patients.3 The concept of treatment for ischemic injury…

Introduction Thyroid cancer (TC) is a common endocrine malignancy with a rapidly increasing incidence worldwide, and the estimated new cases and deaths are notably higher in women than in men.1 Papillary thyroid carcinoma (PTC) is identified as the most common pathological type of TC, and accounts for approximately 80–85% of…

Event listing from University of Pittsburgh: Wednesday, September 15 from 10:00 AM to 4:00 PM This workshop will focus on Gene Expression Omnibus (GEO) repository. We will learn how to find high throughput gene expression studies – bulk RNA-seq/ scRNA-seq /microarray from GEO, retrieve gene expression count data and generate…

Event listing from University of Pittsburgh: Wednesday, September 15 from 10:00 AM to 4:00 PM This workshop will focus on Gene Expression Omnibus (GEO) repository. We will learn how to find high throughput gene expression studies – bulk RNA-seq/ scRNA-seq /microarray from GEO, retrieve gene expression count data and generate…

DOI: 10.18129/B9.bioc.GEOexplorer     This is the development version of GEOexplorer; to use it, please install the devel version of Bioconductor. GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation Bioconductor version: Development (3.14) GEOexplorer is a Shiny app that enables exploratory data analysis and differential gene expression of…

Can you analyze in GEO2R? => No, because this is RNA-seq and not microarrays. You are lucky thought that the authors seem to provide raw counts so you can easily fede them into DESeq2. Here is a code suggestion, for details please read the DESeq2 vignette extensively, it contains answers…