differential expression of geodataset using limma (input files)
Hello
My question after I download Geo soft files how I prepare the file to be suitable as input for limma package? I have read the manual but I could not find what I want??
r
gene
• 1,175 views
•
link
updated
by
Ram
4.5K
• |
written
by
firstorthopedicdoctor
3
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
r script is not working in snakemake
written by firstorthopedicdoctor 3Hi everyone, I created a snake file to download GEO datasets, I get this error message rule download: output: downloads/GSE67311.tar jobid: 0 /bin/sh: 1: 1: …
-
Illumina HumanHT-12 V4.0 expression beadchip
written by zelda 5I'm quite new to the bioinformatics world and just started working with the GEO data set GSE119600. My intention is to extract deferentially expressed genes …
-
How to do FPKM differential analysis?
written by zhaoliang0302 5Hello, I want to do diffrential analysis on rnaseq **FPKM** data (can't get **count**). DEseq and edgR need raw count as input, so how should …
-
Differential gene Expression analysis
written by sujasubramanian 7hello Davis, As you said early i analyse Affymetrix gene chip microarray data set with limma package, but after log transform of .soft file i …
-
Clinical data from GEO
written by landscape95 19Dear everyone, I am doing analysis from GEO database, I download the soft files, extract the expression matrix of probes-to-sample but I don't know where …
-
Download SRA files for a specific Transcription factor (e.g GATA3) from GEO
written by elpavloss2 0Hi!, I want to download several SRA files from different GEO studies, both the input and the replicates data. The last month I spent a …
-
How to Normalize the Microarray Data Obtained from ncbi?
written by pankajnarula84 1I have micro array data in GSE format from http://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE1739. My simple question is how to normalize this data ? All I could see was …
-
visualize tiling array file to IGB
written by catherine 25Hi 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, …
-
Gene Expression File And Gene Regulatory Network
written by someone 0<p>Hello, I wrote a program that receive gene expression file (.SOFT) and give Gene regulatory network (inference it)</p> <p><a href='http://www.ncbi.nlm.nih.gov/geo/info/soft2.htmlhttp://www.ncbi.nlm.nih.gov/geo/info/soft2.html'>click here to see the definition …
-
How To Find Sample Information From Srr Labels In Geo?
written by user 96From GEO one can download SRR* files (ending in .sra) of illumina data that can be extracted as fastq with `fastq-dump`. how can the sample …
Like in your first question, please add details. What datatype is this (methylation, expression array, SNP), which dataset is it, and what is the problem. limma documentation is extensive and should cover like 99.9% of questions one might have. Please be more specific. Also, please use
Questionwhen posting, notForum.[[ Please read before posting a question ::: How To Ask A Good Question ]]