Search
Question: odd results "No enrichment found in any of gene cluster"
0
gravatar for joseph
4 months ago by
joseph40
joseph40 wrote:

I have two gene list as below, one of them is able to obtain an enriched KEGG pathway, the other one cannot.

I consolidate them to one list, and carry on the KEGG enrichment, none of pathway has been found.

The link of .Rdata of these lists, please use list, list_edge, list_limma to access.

https://bri.box.com/s/apc0nwdd57xymhatnngwg01w415rl2me

 

list_limma = list(doublePos_vs_singlePos_limma = DEG_doublePos_vs_singlePos_limma$ENTREZID,
                  doublePos_vs_singlePos_limma_Up = DEG_doublePos_vs_singlePos_limma_Up$ENTREZID,
                  doublePos_vs_singlePos_limma_Down  = DEG_doublePos_vs_singlePos_limma_Down$ENTREZID,
                  doublePos_vs_doubleNeg_limma = DEG_doublePos_vs_doubleNeg_limma$ENTREZID,
                  doublePos_vs_doubleNeg_limma_Up = DEG_doublePos_vs_doubleNeg_limma_Up$ENTREZID,
                  doublePos_vs_doubleNeg_limma_Down = DEG_doublePos_vs_doubleNeg_limma_Down$ENTREZID)

list_edge = list(doublePos_vs_singlePos_edge = DEG_doublePos_vs_singlePos_edge$table$ENTREZID,
                 doublePos_vs_singlePos_edge_Up = DEG_doublePos_vs_singlePos_edge_Up$table$ENTREZID,
                 doublePos_vs_singlePos_edge_Down = DEG_doublePos_vs_singlePos_edge_Down$table$ENTREZID,
                 doublePos_vs_doubleNeg_edge = DEG_doublePos_vs_doubleNeg_edge$table$ENTREZID,
                 doublePos_vs_doubleNeg_edge_Up = DEG_doublePos_vs_doubleNeg_edge_Up$table$ENTREZID,
                 doublePos_vs_doubleNeg_edge_Down = DEG_doublePos_vs_doubleNeg_edge_Down$table$ENTREZID)

levels(list_limma) = c("doublePos_vs_singlePos","doublePos_vs_singlePos_Up","doublePos_vs_singlePos_Down",
                      "doublePos_vs_doubleNeg","doublePos_vs_doubleNeg_Up","doublePos_vs_doubleNeg_Down")

levels(list_edge) = c("doublePos_vs_singlePos","doublePos_vs_singlePos_Up","doublePos_vs_singlePos_Down",
                      "doublePos_vs_doubleNeg","doublePos_vs_doubleNeg_Up","doublePos_vs_doubleNeg_Down")

list = list(doublePos_vs_singlePos = c(DEG_doublePos_vs_singlePos_limma$ENTREZID,DEG_doublePos_vs_singlePos_edge$table$ENTREZID),
            doublePos_vs_singlePos_Up = c(DEG_doublePos_vs_singlePos_limma_Up$ENTREZID,DEG_doublePos_vs_singlePos_edge_Up$table$ENTREZID),
            doublePos_vs_singlePos_Down  = c(DEG_doublePos_vs_singlePos_limma_Down$ENTREZID,DEG_doublePos_vs_singlePos_edge_Down$table$ENTREZID),
            doublePos_vs_doubleNeg = c(DEG_doublePos_vs_doubleNeg_limma$ENTREZID,DEG_doublePos_vs_doubleNeg_edge$table$ENTREZID),
            doublePos_vs_doubleNeg_Up = c(DEG_doublePos_vs_doubleNeg_limma_Up$ENTREZID,DEG_doublePos_vs_doubleNeg_edge_Up$table$ENTREZID),
            doublePos_vs_doubleNeg_Down = c(DEG_doublePos_vs_doubleNeg_limma_Down$ENTREZID,DEG_doublePos_vs_doubleNeg_edge_Down$table$ENTREZID))

levels(list) = c("doublePos_vs_singlePos","doublePos_vs_singlePos_Up","doublePos_vs_singlePos_Down",
                 "doublePos_vs_doubleNeg","doublePos_vs_doubleNeg_Up","doublePos_vs_doubleNeg_Down")

 

CompKEGG_limma <- compareCluster(geneCluster = list_limma, fun = "enrichKEGG",organism="hsa", pvalueCutoff=1)

CompKEGG_edge <- compareCluster(geneCluster = list_edge, fun = "enrichKEGG",organism="hsa", pvalueCutoff=1)

CompKEGG <- compareCluster(geneCluster = list, fun = "enrichKEGG",organism="hsa", pvalueCutoff=1)

 

ADD COMMENTlink modified 4 months ago by Guangchuang Yu800 • written 4 months ago by joseph40
0
gravatar for Guangchuang Yu
4 months ago by
Hong Kong
Guangchuang Yu800 wrote:

your code is not reproducible.

pls see also C: Subset of genes can find a term but whole set cannot.

ADD COMMENTlink written 4 months ago by Guangchuang Yu800

I can understand the principle of gene enrichment. I just so surprised about nonpathway can be matched because the list is approx 1000+, even without significance (I set pvalueCutoff = 1), should have some gene match to KEGG pathway. I doubt if the list feature causes the problem? I check several times, not conclude, so have to raise the question.

What's the error do you get when you reproduce my code?

ADD REPLYlink modified 4 months ago • written 4 months ago by joseph40

> CompKEGG <- compareCluster(geneCluster = list, fun = "enrichKEGG",organism="hsa", pvalueCutoff=1)
Error in compareCluster(geneCluster = list, fun = "enrichKEGG", organism = "hsa",  :
  No enrichment found in any of gene cluster, please check your input...
> CompKEGG <- compareCluster(geneCluster = list, fun = "enrichKEGG",organism="hsa", pvalueCutoff=1, qvalueCutoff=1)
> head(CompKEGG, 2)
                 Cluster       ID
1 doublePos_vs_singlePos hsa04141
2 doublePos_vs_singlePos hsa05120
                                                 Description GeneRatio  BgRatio
1                Protein processing in endoplasmic reticulum    25/626 166/7271
2 Epithelial cell signaling in Helicobacter pylori infection    13/626  68/7271
       pvalue  p.adjust    qvalue
1 0.003948754 0.6872773 0.6813311
2 0.004707379 0.6872773 0.6813311
                                                                                                                                      geneID
1 10802/3320/29979/22926/23645/10483/6746/27102/10484/824/9373/6747/9532/7353/23471/51726/7466/9978/54788/64215/5611/10273/80343/56886/80700
2                                                                           102/5803/3576/245973/8992/1445/5336/83700/3551/526/523/5058/1956
  Count
1    25
2    13
>
>

ADD REPLYlink written 4 months ago by Guangchuang Yu800

In the compareCluster documents,  I can't find the default qvalueCutoff setting. In the above situation, no enrichment can be found when pvalueCutoff = 1, but 2 enrichment show up when set q = 1. I suppose the default q had been set less than 1. Is that right?

ADD REPLYlink written 4 months ago by joseph40

yes, and the parameter list of compareCluster depends on the fun parameter. In your case, all enrichKEGG parameters can be passed to compareCluster.

ADD REPLYlink modified 4 months ago • written 4 months ago by Guangchuang Yu800
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 192 users visited in the last hour