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9.3 years ago
f.dehghanian68
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30
I'm working on microarray data of GEO. Many data are in .txt format. how can I use them for analysis. Is there any way to convert .txt format to .CEL format?
If you are using R, have you tried the GEOquery bioconductor package?
I used this package for .soft format. Can I use this for loading .txt file in R?
R can easily read most tab-delimited files.
read.delim()orread.table()will most likely work just fine.Yes of course, but is there any method to normalize .txt data in R or other softwares? I shoud normalize these .txt data for further analysis???
About the Soft files: Should I normalize this data or they are normalized? Can I normalize these files in R?
They are normalized, but you can't always tell how. Most of the times it's not in log. Look at GEOquery vignette, there's a description of how to read soft files of all the GSMs and use the data you want instead of taking the txt matrix where you don't know or not sure what the data is.
As a general rule, use GSEMatrix files instead of the parsing code in the GEOquery vignette. Only in unusual circumstances would you need to parse things out of individual GSMs.
Thank you very much for your help. I read soft file in R using GEOquery. Can I normalize this data using other methods? Actually I normalize .CEL easily in R, but this dataset just has Soft and txt file. I need to normalize soft file using method in log? Is there any possible way to do this?
The
log2()function in R takes the log base 2.Actually I'm also facing same problem. I have .txt files or soft files. How did you normalize soft files or .txt files. Please reply.
I am facing the same problem. I have text files only from GEO. How did you do the analysis with these files? Please reply