structure of SOFT files

Hi!

I have a GEO file with .soft format, how do I know that this file is one or two channel? can I read SOFT files with read.maimages or ReadAffy functions? The SOFT file structure is confusing me!

Thank you!

.soft r geo

• 4,026 views • link

updated 4.0 years ago by Ram

• written 10.5 years ago by vahideh •

1 answer

See here for importing GEO files into R:

http://bioconductor.org/packages/GEOquery

• 0 views • link

written 10.5 years ago by Sean Davis

Thanks Davis!

I already work with GEOquery, but however, I don't handle it!

• 0 views • link

written 10.5 years ago by vahideh •

What problems did you have?

• 0 views • link

updated 6.6 years ago by Ram

• written 10.5 years ago by Sean Davis

I downloaded several GSE files with SOFT format by GEOquery package, then I must implement QC on them. since, As I understood, Quality Control performed differentially between Affymetrix, Agilent and Illumina arrays, so I need to know that I work with which array, and how I Implemented QC on it!

• 0 views • link

updated 6.6 years ago by Ram

• written 10.5 years ago by vahideh •

More posts like this

convert .txt file to fasta format
written 6.4 years ago by ravi.eshwari •

Hi, I have downloaded .txt files from supplementary data of GEO database . I want to convert these txt format files to fasta format. Can …
Microarray data with Agilent platform
written 6.8 years ago by sh •

Hello every one I downloaded "series matrix file" Microarray with Agilent platform, there are some issues: 1.how should i know that this is one color/channel …
how to compare 2 rna-seq counts with each other by python
written 7.4 years ago by ali.hakimzadeh •

Hi, I have 50 samples with a gen counts from an RNA-seq that I want to compare my counts with another one. I have two …
Problem for reading annotation file for GPL10999_family.soft
written 7.4 years ago by modarzi

Hi, I have downloaded RNA-seq data from [GSE45510][1]. for annotation file I have downloaded [SOFT formatted family file(s)][2] from GPL10999. Now, I want to read …
GEO (NCBI) confusing data
written 10.5 years ago by silas008

Hi, I'm have some problems with one data shared on GEO: In this link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19414, we can find a list of 26 samples. Clicking on …
The difference between Affymetrix and Agilent
written 10.6 years ago by vahideh •

Hi! How can I know that my array in the Limma package is Affymetrix or Agilent? Thank you
Normalizing soft files using log based methods
written 11.0 years ago by f.dehghanian68 •

I can read soft files in R using GEOquery. They are normalized, but we can't always tell how. Most of the times it's not in …
Downloading .CEL files from GEO
written 11.3 years ago by alara •

Hi, I would like to download all .CEL files from samples with specific characteristics. For example, I need to obtain **all** .CEL files with "normal …
visualize tiling array file to IGB
written 11.8 years ago by catherine

Hi everyone, I want to compare my chip-seq data and GEO tiling array data in IGB. This is my first time dealing with tiling array, …
Extracting Information From Geo Soft Files
written 14.1 years ago by Layla •

<p>Hi: I am working with the soft files obtained from GEO from specific diseases. The question that I have is that if there is an …