Question: How to fix the error "Error in fastmatch::fmatch(x, y) : ..." ?
1
gravatar for loicborcard01
8 weeks ago by
loicborcard0110 wrote:

Hello everyone, I am running GSVA on an expressionset and it is giving this error, I have been looking for a way to fix it but I did not find anything. Does anybody know what's causing this and how I could fix it?

No annotation package name available in the input 'ExpressionSet' object 'expr'.
Attempting to directly match identifiers in 'expr' to gene sets.
Error in fastmatch::fmatch(x, y) : 
  no method for coercing this S4 class to a vector
In addition: Warning messages:
1: In .filterFeatures(expr, method) :
  7098 genes with constant expression values throuhgout the samples.
2: In .filterFeatures(expr, method) :
  Since argument method!="ssgsea", genes with constant expression values are discarded.

Here is how I created my expression set, I started from a countfile

head(sampleinfos_day3)
day animalid treatment
1 Day 3      G14      MOCK
2 Day 3      G15      MOCK
3 Day 3      G16      MOCK
4 Day 3      G17      MOCK
5 Day 3      G18      MOCK
6 Day 3      G19      MOCK
dim(sampleinfos_day3)
[1] 24  3
head(eset_matrix)
                      1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16
ENSSSCG00000037372  131  106   98  112   95   77  161   39  137  115  163  104  221  160  117  111
ENSSSCG00000027257 2309 1913 1515 2024 1627 1282 1775 2131 2395 1836 1874 1902 3205 2632 1950 1891
ENSSSCG00000029697  973  643  691  550  701  479  998  696  864  871 1363  763 1197 1036  777  786
ENSSSCG00000027274   12    4    6    1    7    6    8    0    9    4   13    4    3    3    4    5
ENSSSCG00000027726   32   68   24   67   11   18   16   62   89   10   40   16   89   90  182   24
ENSSSCG00000033475    1    1    0    0    0    0    2    0    1    1    2    0    0    0    0    0 


phenoData<-new("AnnotatedDataFrame",data=sampleinfos_day3)
eset<-ExpressionSet(assayData = eset_matrix,phenoData = phenoData)

Thank you very much

R rna-seq gsva enrichment • 135 views
ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by loicborcard0110
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