Question: .txt format file in GEO
1
gravatar for f.dehghanian68
4.1 years ago by
‌Iran
f.dehghanian6830 wrote:

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?

R • 2.5k views
ADD COMMENTlink modified 4.1 years ago by Sean Davis25k • written 4.1 years ago by f.dehghanian6830
1

If you are using R, have you tried the GEOquery bioconductor package?  

ADD REPLYlink written 4.1 years ago by Sean Davis25k

I usead this package for .soft format. Can I use this for loading .txt file in R? 

ADD REPLYlink written 4.1 years ago by f.dehghanian6830

R can easily read most tab-delimited files.  read.delim() or read.table() will most likely work just fine.

ADD REPLYlink written 4.1 years ago by Sean Davis25k

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???

ADD REPLYlink written 4.1 years ago by f.dehghanian6830

About the Soft files: Should I normalize this data or they are normalized? Can I normalize these files in R?

ADD REPLYlink written 4.1 years ago by f.dehghanian6830

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.

ADD REPLYlink written 4.1 years ago by Asaf6.1k

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.

ADD REPLYlink written 4.1 years ago by Sean Davis25k

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?

ADD REPLYlink written 4.1 years ago by f.dehghanian6830

The log2() function in R takes the log base 2.

ADD REPLYlink written 4.1 years ago by Sean Davis25k

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.

ADD REPLYlink written 2.6 years ago by garimav890
4
gravatar for Sean Davis
4.1 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

To answer your question, no, there is not a way to convert .txt to .cel.

 

ADD COMMENTlink written 4.1 years ago by Sean Davis25k
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