Question: Singscore get some NA values result, normal?
0
gravatar for MatthewP
18 months ago by
MatthewP880
China
MatthewP880 wrote:

Hello, I only have one gene set, not up and down. My code didn't set downSet = NULL because this will cause bug.

epi_score <- simpleScore(rankData, upSet=epi_gene, knownDirection=FALSE)

My epi_score has some NA score, how to explain no score for some samples? Thanks.

> tail(epi_score)
          TotalScore TotalDispersion
GSM764972         NA              NA
GSM764973         NA              NA
GSM764974         NA              NA
GSM764975         NA              NA
GSM764976         NA              NA
GSM764977         NA              NA

My gene set size is 140 and only 1 not in expression matrix.
Also I have another gene set named Mes with the same processing method, and get NA at same samples.

> filter(emt_score2, is.na(Epi) | is.na(Mes))
# A tibble: 79 x 5
   Sample      Epi   Mes `age:ch1` `Sex:ch1`
   <chr>     <dbl> <dbl> <chr>     <chr>    
 1 GSM764899    NA    NA 60-88     M        
 2 GSM764900    NA    NA 60-88     M        
 3 GSM764901    NA    NA 60-88     M        
 4 GSM764902    NA    NA 60-88     F        
 5 GSM764903    NA    NA 50-59     M        
 6 GSM764904    NA    NA 60-88     M        
 7 GSM764905    NA    NA 40-49     F        
 8 GSM764906    NA    NA 60-88     M        
 9 GSM764907    NA    NA 50-59     F        
10 GSM764908    NA    NA 60-88     F        
# … with 69 more rows
singscore • 363 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by MatthewP880
1
gravatar for MatthewP
18 months ago by
MatthewP880
China
MatthewP880 wrote:

Problem solved! Nothing to do with function simpleScore result. The problem is some NA values expression data in those samples(1 gene).

ADD COMMENTlink written 18 months ago by MatthewP880
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