Pathway analysis using GAGE returns all NA values
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microPhD • 0
@microphd-24044
Last seen 3.8 years ago

I have RNA-seq data that I'm trying to run pathway analysis on. I'm using the GAGE R package. When I run the gage function, all the values are NA and I don't understand why. The only thing that I can think of is that my dataset does have some genes in it that are not in the reference gene set. This is because my organism was re-annotated by NCBI and I had to convert the new locus tags to old locus tags, but there are some new locus tags that do not have old locus tags. I would think that GAGE would just disregard these new genes, but maybe they are messing up the analysis somehow.

# Reference gene set
kg.bth = kegg.gsets(species = "bth", id.type = "kegg")

# RNA-seq count data
> head(data,2)
        RN11 RN12 RN14 RN16 RN17 RN19 RN21 RN22 RN24 RN31 RN32 RN34 RN36 RN37 RN39 RN46 RN47 RN49 RN51 RN52
BT_0001    5    4   42    3    5   25    1    6   12    8    8   18    7   11   20    6   17   17   10    2
BT_0002    2    0   11    2    5   10    4   10    2    8   16   14    6    7   14    6   14    6   20    0
        RN54 RN61 RN62 RN64 RN13 RN15 RN18 RN20 RN23 RN25 RN33 RN35 RN40 RN48 RN50 RN53 RN55 RN63 RN65
BT_0001   13   12   12   12    3   25   33   23    9   12   13   24   17   22    6   23   74   31   21
BT_0002    8    9   10    7    6    9   16    8    8    4    2   14    0   10   10   10   22   20    5

# Analysis
gage <- gage(data, kg.bth,
             ref= (1:24),
             samp = (25:39),
             same.dir = FALSE,
             compare = "unpaired")

> gage
$greater
           p.geomean stat.mean p.val q.val set.size RN13 RN15 RN18 RN20 RN23 RN25 RN33 RN35 RN40 RN48 RN50
kg.sets           NA       NaN    NA    NA        1   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA
sigmet.idx        NA       NaN    NA    NA        0   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA
sig.idx           NA       NaN    NA    NA        0   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA
met.idx           NA       NaN    NA    NA        0   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA
dise.idx          NA       NaN    NA    NA        0   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA
           RN53 RN55 RN63 RN65
kg.sets      NA   NA   NA   NA
sigmet.idx   NA   NA   NA   NA
sig.idx      NA   NA   NA   NA
met.idx      NA   NA   NA   NA
dise.idx     NA   NA   NA   NA

$stats
           stat.mean RN13 RN15 RN18 RN20 RN23 RN25 RN33 RN35 RN40 RN48 RN50 RN53 RN55 RN63 RN65
kg.sets          NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN
sigmet.idx       NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN
sig.idx          NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN
met.idx          NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN
dise.idx         NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN  NaN
gage rna-seq pathwayanalysis • 1.5k views
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I am not the developer of this package. I assume that you can successfully run these functions by following the vignette?

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Did you solve the issue? I'm running into the same problem now...

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