own genelist; too dump top proceed

[mocherry]

Dear Clusterprofiler-Team,

being quite new to R I am struggling with the following problem:
I have prepared a comma-delimited Excel file (.csv) with gene expression data: first column Gene Symbol, second column FC as described.
It the looks like this (first three rows):
ID,FC
CXCL3,12.95135115
MMP3,12.40100107
IL6,11.1025565

Then I run:
d <- read.csv("C:/users/kirsch/Desktop/clusterprofiler.csv")
geneList = d[,2]
names(geneList) = as.character(d[,1])
geneList = sort(geneList, decreasing = TRUE)
gene <- names(geneList)[abs(geneList) > 2]
ggo <- groupGO(gene = gene,
OrgDb = org.Hs.eg.db,
ont = "CC",
level = 3,
readable = TRUE)

#and get the error: Error in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are valid keys for 'ENTREZID'. Please use the keys method to see a listing of valid arguments

I guess I miss something important or just do not understand enough to solve the problem. Maybe someone can help.
Thanks and ebst,
Matthias

[huerqiang]

Use ?groupGO to get the doc of this function. Since your gene id is gene symbol, you should add the parameter: keyType = SYMBOL .

[mocherry]

Dear Huerqiang,

I have added keyType = "SYMBOL" to the script:

d <- read.csv("C:/users/kirsch/Desktop/clusterprofiler.csv")
geneList = d[,2]
names(geneList) = as.character(d[,1])
geneList = sort(geneList, decreasing = TRUE)
gene <- names(geneList)[abs(geneList) > 2]
ggo <- groupGO(gene = gene,
OrgDb = org.Hs.eg.db,
keyType = "SYMBOL",
ont = "CC",
level = 3,
readable = TRUE)

and get the following error:
Error in names(x) <- value :
'names' attribute [2] must be the same length as the vector [1]

The geneList produced by this script looks like this:
Type value
CxCL3 double(1) 12.95135

I really do not know where to start to solve this. Admittedly, I am rather inexperienced with R and new to ClusterProfiler.

Help would really be appreciated,
Matthias

[huerqiang]

Please send the "clusterprofiler.csv" file to me: [email protected], and I will give the suitable code.