Question: How to analyse TXT format microarray data
0
gravatar for afli
8 weeks ago by
afli170
China, Beijing, IGDB
afli170 wrote:

Dear friend, I want to analyse some microarray data in TXT format. I analyse CEL format data previously, but this time I could hardly find any procedures to analyse the TXT format data. My purpose is to find the differential genes between each two samples. Can someone tell me how to analyse the TXT format data? Its link is: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE39429. Thank you!

txt microarray • 141 views
ADD COMMENTlink modified 8 weeks ago by Friederike3.7k • written 8 weeks ago by afli170

Did you take a look at this README which describes how the data was generated?

ADD REPLYlink written 8 weeks ago by genomax65k
2
gravatar for Benn
8 weeks ago by
Benn6.6k
Netherlands
Benn6.6k wrote:

Before you can analyze data, you need to know more than only the format (TXT). TXT means that it is a text file, tab delimited probably. That is not microarray specific, TXT files are used by many computer programs. So please read more about the experiment GSE39429 itself first, it seems to be an Agilent 4x44K array. Try a tutorial if Agilent array doesn't ring a bell, or try to read some user's guides (limma would be a good choice). Good luck.

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by Benn6.6k
2
gravatar for Friederike
8 weeks ago by
Friederike3.7k
United States
Friederike3.7k wrote:

Kevin addressed this question before; in short: the text files usually contain normalized log2FC values, but not always. Once you know what the values represent in your project of interest, you may want to give the GEOquery package a try as it allows for direct download of the data and offers instructions on how to plug those into the ExpressionSet environment of the R bioconductor packages that you may already be familiar with.

ADD COMMENTlink written 8 weeks ago by Friederike3.7k
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