Entering edit mode
4.3 years ago
loicborcard01
▴
40
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