Hello,
I have 1 csv file containing 200, 100 of 'group A' and 100 of 'group B'
looking like this:
sample1 sample2 sample3 samepl4 sample5 etc...
groupA groupA groupA groupA groupA etc... groupB groupB groupB
probe1 7.823 3.45645 4.2349 2.2349 5.23498 3.45645 2.2139 3.4534
probe2 9.53 3.2340 3.0980 3.8858 3.83493 3.85673 2.2399 3.2340
probe3 8.823 9.45645 3.2349 2.2349 5.23498 8.823 3.2349 9.59
etc...
Using Limma in R, I want to know which genes are differentially expressed between the 2 groups. Seems very simple to me, but when I look up tutorials everything seems way to complicated for what I want. How should I approach this?
The limma manual is your friend: https://www.bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf
This manual right, where is the data they are working with? They have all these examples but the data is nowhere nowhere to be found. Where is "targets.txt" for example or "eset"?
It is quite straightforward to do w/o the example data, you just need to keep trying.
Really? From the first two examples alone:
Example 1:
In this example we assume that the data is provided as a GAL file called fish.gal and raw SPOT output files and that these files are in the current working directory. The data used for this case study can be downloaded from http://bioinf.wehi.edu.au/limmaGUI/DataSets.html
Example 2:
In this section we consider a case study where two RNA sources are compared through a common reference RNA. The analysis of the log-ratios involves a two-sample comparison of means for each gene.
In this example we assume that the data is available as an RGList in the data file Apoa1.RData. The data used for this case study can be downloaded from http://bioinf.wehi.edu.au/limma
And the example starting on page 40 should be instructive. You shouldn't actually need any data to follow the example, as it's pretty straightforward.