Question: GOplot and making circle_dat out of microarray and DAVID data
gravatar for farzaneafzali
19 months ago by
farzaneafzali70 wrote:

I am going to use GOplot package of R to visualize my ontology results out of microarray analysis of cancerous and normal tissues. I have problem with using this code:

circ <- circle_dat(EC$david, EC$genelist)

I have two text files. One for microarray with columns namely: ID, adj.P.Val, logFC, AveExpr, B, and t. Another file is for david data with columns of: Category, ID, Term, PValue, and Genes. I import these two files into R-studio with these codes:

genelist <- read.csv("genelist.txt", sep = "\t", header = TRUE)
david <- read.csv("BP1.txt", sep = "\t", header = TRUE)

But when I am going to build the circle_dat out of these with this code:

circ <- circle_dat(david, genelist)

I get the error of:

Error in data.frame(category = rep(as.character(terms$category), count),  : 
  arguments imply differing number of rows: 8765, 0

How should I form the circle_dat for my data. By the way, I am just a biologist and does not have any strong background in programming, so please kindly give me a code for this because I cannot understand the programming explanations. I have already saw this link and could not understand anything :( Thank you.

ADD COMMENTlink modified 19 months ago by MasMarius10 • written 19 months ago by farzaneafzali70

Looks like your data has 'Category' whereas the function looks for 'category' (small 'c').

You should also look into your objects to see how they look. It is a good habit to have. For example:


As a side note, I posted a tutorial for plotting DAVID results: Clustering of DAVID gene enrichment results from gene expression studies

ADD REPLYlink modified 19 months ago • written 19 months ago by Kevin Blighe66k

Thanks a lot Kevin. I've already figured out how to plot my data via GOplot and now I am going to make a tutorial for Youtube. I will post the link later here so everyone can use it especially biologists. By the way, I loved your way of plotting, thank you for introducing that to me.

ADD REPLYlink written 19 months ago by farzaneafzali70

@farzaneafzali could you also share it by written? It would be much appreciated. Thanks in advance!

ADD REPLYlink written 19 months ago by MasMarius10

excuse me,can you tell me how to solve the problem?

ADD REPLYlink written 3 months ago by 18304160190

Please elaborate more on the problem that you are facing. Open a new question, if you feel that is needed, too.

ADD REPLYlink written 3 months ago by Kevin Blighe66k
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