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!
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.
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.