End-to-end analysis of a gene microarray dataset | bespokeDS
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- čas přidán 8. 06. 2024
- For this month's meet-up, we will analyse a microarray dataset from the Gene Expression Omnibus (GEO). We will go through the code provided by the GEO2R tool for comparing gene expression between two groups, and explain what each line does. Although it doesn't offer the same flexibility that doing the analysis in R provides, GEO2R is a useful point-and-click tool for simple group comparisons.
In this video You analyze the One GSE data though R. My question is how we analyze the two GSE datasets through R . We select the affected samples from one data and control samples from the second GSE..
Can you please make a video about the limma package? Especially the model matrix design. I got confused!
This is a super tricky concept! We recently made a video on this that I hope clears things up a little - czcams.com/video/HWOllPTpnq0/video.html
How can we get gene symbol when there is no column specifying it. I have a column "GB_LIST"-anyway to get it from there?
Just at 16:55 I think you initially meant to say there was no need for log2 transformation, since LogC was FALSE. Thanks for the very useful technical tips and guidelines.
Can you guide me about the analysis of two of 2 GSE datasets..
Hello, everything worked fine for me until the last function where i tried to save the table, i get the message :
Error in `[.data.frame`(x, r, vars, drop = drop) :
undefined columns selected
i checked, and i haven't made any mistakes in the code. What could be the problem? is there any other way to save the table??
Hi when i run fit2 on my contrast matrix i get a error saying row name of contrast does not math row name of coefficient . Can you help me understand which part is my mistake?
hey! I am confused how the grouping works
We made a follow-up video that I hope makes this a little clearer - czcams.com/video/HWOllPTpnq0/video.html