Question: Where to find annotation infos for my Expressionset?
0
gravatar for loicborcard01
3 months ago by
loicborcard0110 wrote:

Hello, I am running gsva on an ExpressionSet and a Geneset.collection that I created myself. And I get the error message written in red down below. I don't understand what's missing.

`> eset
 ExpressionSet (storageMode: lockedEnvironment)
 assayData: 25880 features, 24 samples 
 element names: exprs 
 protocolData: none
 phenoData
sampleNames: 1 2 ... 24 (24 total)
varLabels: day animalid treatment
varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation:  `
`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.
rna-seq gsva R • 244 views
ADD COMMENTlink modified 8 weeks ago by Biostar ♦♦ 20 • written 3 months ago by loicborcard0110

How did you create the expressionSet object? Did you create an annotation creating the object?

Please post you code and more information about your expressionSet so we have the necessary information to help you.

ADD REPLYlink written 3 months ago by h.mon31k

Now that you saw how I created my expressionset you think you could help me?

ADD REPLYlink written 3 months ago by loicborcard0110

You have not shown your ssgsea command anywhere? - you may need to use exprs(eset)

ADD REPLYlink written 8 weeks ago by Kevin Blighe68k
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)
ADD REPLYlink modified 3 months ago by h.mon31k • written 3 months ago by loicborcard0110

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

ADD REPLYlink written 3 months ago by GenoMax92k

Thank you, I am trying to use it properly but it turned out red idk why.

ADD REPLYlink modified 3 months ago • written 3 months ago by loicborcard0110

You don't need to use backticks if you are going to use the code (101) button that is highlighted in the screencap above.

ADD REPLYlink written 3 months ago by GenoMax92k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1553 users visited in the last hour