ClusterProfiler - How to : input file, groupGo, enrichGo
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Mataivic • 0
@mataivic-12506
Last seen 4.3 years ago

Hello everybody,

I am a student currenty trying to learn how to use clusterProfiler. I figured out a few things but I still have many issues, (I apologize, I know that usually its' better to ask only one question), since I also have a lack of knowledge in this field of biology.

First, I am not sure about the format of the input file : I'm trying with a txt file shaped like this :

Ensembl_Gene_ID        Gene_Symbol        log2FC_DeSeq    p_DeSeq        padj_DeSeq    
ENSG00000090339       ICAM1                  6,5146051234      0                   0
ENSG00000108691       CCL2                    6,3686974669      0                   0
ENSG00000118503       TNFAIP3               4,142184042        0                   0

etc...

I'm still not sure if I'm using the good table of data, because the groupGo and enrichGo functions do not work.

I did :

data <- read.table("human_retine.txt", header=TRUE, dec=",")

# Gene Ontology classification
genes <- data$Ensembl_Gene_ID
genes <- as.character(genes)

ggo <- groupGO(gene = genes, organism = "human", ont = "BP", level = 3,
               readable = TRUE)

# Enrich GO
genes<-data$Ensembl_Gene_ID[abs(data$log2FC_DeSeq)>2]
ego <- enrichGO(genes , organism= "human", ont= "CC", pAdjustMethod="BH", pvalueCutoff=0.1, qvalueCutoff=0.5, readable= TRUE)

First, I had the following error when launching groupGo :

Error in validObject(.Object) :
  invalid class “groupGOResult” object: invalid object for slot "gene" in class "groupGOResult": got class "factor", should be or extend class "character"

So I add the as.character line, which gave me :

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

Then, when I launch enrichGo, the result is [NA], wheter or not the as.character function has been called.

So, it is really messy for me ... what am I doing wrong ? I am reading the docs but I don't understand all of it.

Thanks !

 

clusterprofiler input files error help • 3.4k views
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The last error tells you to use ENTREZID, so convert your ensemble gene annotation to ENTREZIDs first (see manual, like Guangchuang Yu said already).

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ENSEMBL ID is also supported if user specify keytype = 'ENSEMBL', which is documented in vignette.

Vignette already answered all the issues posted here.

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Great! I wasn't aware of the keytype argument, yet!

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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 7 months ago
China/Guangzhou/Southern Medical Univer…

First of all, you are using an out-dated version of clusterProfiler, see the output of rvcheck::check_bioc('clusterProfiler').

You need to upgrade it to latest release version.

Please read the vignette of latest release version, you will find the answer of your question.

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