Keep getting NaN Values in GAGE analysis of KEGG pathways
0
0
Entering edit mode
@owendonohoe-18047
Last seen 21 months ago

Hi 

Below is a sample of my output from Deseq2. IDs are Entrez, I'd lke to use them to do pathway analysis with GAGE

 

> head(deseq2.res)
log2 fold change (MLE): Infection.Type Susceptible.Intected vs Susceptible.Non.Intected 
Wald test p-value: Infection.Type Susceptible.Intected vs Susceptible.Non.Intected 
DataFrame with 6 rows and 7 columns

           baseMean log2FoldChange     lfcSE       stat      pvalue
          <numeric>      <numeric> <numeric>  <numeric>   <numeric>
105333743 15.835268      2.5407024 1.0263944  2.4753665 0.013309952
105333775  4.730554     -0.7931533 1.5979284 -0.4963635 0.619637996
105334150  7.294318     -0.8172277 1.1966521 -0.6829284 0.494652087
105334256  9.666313     -1.4400413 0.7404432 -1.9448370 0.051794597
105334292 12.375891      0.2330889 1.0664642  0.2185623 0.826990998
105334343  4.961679     -5.1985084 1.3283420 -3.9135316 0.000090956
                  padj    weight
             <numeric> <numeric>
105333743 0.0341735692         1
105333775 0.7239544639         1
105334150 0.6144798713         1
105334256 0.1049475388         1
105334292 0.8813991828         1
105334343 0.0004646112         1

I prepared fold change data and gene set for GAGE as such

deseq2.fc=deseq2.res$log2FoldChange
names(deseq2.fc)=rownames(deseq2.res)
exp.fc=deseq2.fc

> head(exp.fc)
 105333743  105333775  105334150  105334256  105334292  105334343 
 2.5407024 -0.7931533 -0.8172277 -1.4400413  0.2330889 -5.1985084

> str(exp.fc)
 Named num [1:13190] 2.541 -0.793 -0.817 -1.44 0.233 ..
 - attr(*, "names")= chr [1:13190] "105333743" "105333775" "105334150" "105334256" ...

>kg.oyster=kegg.gsets(species = "crg", id.type = "kegg")

> head(kg.oyster)
$kg.sets
$kg.sets$`crg00010 Glycolysis / Gluconeogenesis`
 [1] "105317497" "105317783" "105318439" "105318496" "105319260" "105319828"
 [7] "105320252" "105321314" "105322313" "105322747" "105323106" "105323467"
[13] "105323703" "105323969" "105324578" "105325277" "105325828" "105326051"
[19] "105326107" "105326193" "105327683" "105328152" "105330573" "105330800"
[25] "105330845" "105330868" "105330927" "105331349" "105332291" "105332305"
[31] "105332343" "105334225" "105334471" "105335306" "105335383" "105335442"
[37] "105335816" "105335896" "105336470" "105336484" "105336761" "105338126"
[43] "105338756" "105339245" "105339247" "105339502" "105340365" "105340512"
[49] "105343230" "105344389" "105344593" "105345431" "105345955" "105346675"
[55] "105346996" "105347640" "105347662" "105348082" "109620123"

$kg.sets$`crg00020 Citrate cycle (TCA cycle)
[1] "105317044" "105317497" "105319941" "105320391" "105322330" "105323405"
[7] "105326051" "105326107" "105326324" "105326362" "105326646" "105328068"
[13] "105328773" "105328869" "105330227" "105330573" "105331349" "105332143
[19] "105332343" "105333137" "105334026" "105334926" "105335210" "105335901
[25] "105337089" "105338659" "105338756" "105338798" "105339502" "105341248"
[31] "105343391" "105343888" "105345431" "105345932" "105347017" "105349203"

 

However when I use this in GAGE analysis all I gen back are NAs/NaNs ??

 

> fc.kegg.p <- gage(exp.fc, gsets = kg.oyster, same.dir=TRUE)
> lapply(fc.kegg.p, head)
$greater
           p.geomean stat.mean p.val q.val set.size exp1
kg.sets           NA       NaN    NA    NA        0   NA
sigmet.idx        NA       NaN    NA    NA        0   NA
sig.idx           NA       NaN    NA    NA        0   NA
met.idx           NA       NaN    NA    NA        0   NA
dise.idx          NA       NaN    NA    NA        0   NA

$less
           p.geomean stat.mean p.val q.val set.size exp1
kg.sets           NA       NaN    NA    NA        0   NA
sigmet.idx        NA       NaN    NA    NA        0   NA
sig.idx           NA       NaN    NA    NA        0   NA
met.idx           NA       NaN    NA    NA        0   NA
dise.idx          NA       NaN    NA    NA        0   NA

$stats
           stat.mean exp1
kg.sets          NaN   NA
sigmet.idx       NaN   NA
sig.idx          NaN   NA
met.idx          NaN   NA
dise.idx         NaN   NA

 

At the moment I'm unsure why this is happening, I would appreciate any help with this.

KEGG GAGE NaN R DESeq2 • 573 views
ADD COMMENT

Login before adding your answer.

Traffic: 378 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6