Question: GOplot and making circle_dat out of microarray and DAVID data
0
gravatar for farzaneafzali
9 months ago by
farzaneafzali60 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 :( https://stackoverflow.com/questions/29814912/error-replacement-has-x-rows-data-has-y Thank you.

ADD COMMENTlink modified 8 months ago by MasMarius10 • written 9 months ago by farzaneafzali60
1

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:

head(genelist)
head(david)

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 9 months ago • written 9 months ago by Kevin Blighe51k
2

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 9 months ago by farzaneafzali60

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

ADD REPLYlink written 8 months ago by MasMarius10
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