Question

Suggestion for FGSEA and GSEA creation for C57BL/6J Mice

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Gordon • 0

@083bbd83

Last seen 3 hours ago

United States

Hi all,

I am trying to create GSEA and FGSEA for C57BL/6J Mice species. I had created a code for human species, and thought to switch out all human input as mice. However, I ran into some issues,

res <- res %>%
  mutate(rank = rank(log2FoldChange, ties.method = "random")) 
ens2symbol <- AnnotationDbi::select(org.Mm.eg.db,
                                    key=res$row, 
                                    columns="SYMBOL",
                                    keytype="ENTREZID")

Error in .testForValidKeys(x, keys, keytype, fks) : 'keys' must be a character vector

The input of column row is ENSMUSG* gmt pathway is mh.all.v2024.1.Mm.symbols.gmt

Any suggestions?

gsea mice org.Mm.eg.db • 291 views

ADD COMMENT • link updated 2 hours ago by James W. MacDonald 67k • written 16 hours ago by Gordon • 0

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what is the class and values of res$row ?

ADD REPLY • link 7 hours ago shepherl 4.0k

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It appeared as "NULL"

Res input is: "row","baseMean","log2FoldChange","lfcSE","stat","pvalue","padj" Data shows 7 variables with row as first column.

ENSMUSG00000101249 23365.54446 1.411235 0.3365968 4.192657 2.757065e-05 1.026079e-02

ADD REPLY • link 5 hours ago Gordon • 0

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If you get NULL for something in R, it means it's not there. You don't show the head of res, but instead one row, so my guess would be the column is actually named something different like 'Row', or maybe those are the rownames rather than a column.

ADD REPLY • link 4 hours ago James W. MacDonald 67k

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As an example,

> d.f <- data.frame(Row = letters, values = 1:26)
> d.f$row
NULL

ADD REPLY • link 4 hours ago James W. MacDonald 67k

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> head(res)
# A tibble: 6 × 9

row                baseMean log2FoldChange lfcSE  stat        pvalue      padj  rank SYMBOL
  <chr>                 <dbl>          <dbl> <dbl> <dbl>         <dbl>     <dbl> <int> <chr> 
1 ENSMUSG00000101249   23366.           1.41 0.337  4.19 0.0000276     0.0103      123 NA    
2 ENSMUSG00000024610   12719.          -1.96 0.506 -3.87 0.000109      0.0262       91 Cd74  
3 ENSMUSG00000069516    7123.          -2.22 0.374 -5.94 0.00000000281 0.0000115    77 Lyz2  
4 ENSMUSG00000076617    7631.          -1.94 0.355 -5.48 0.0000000437  0.0000813    92 Ighm  
5 ENSMUSG00000076609    7438.          -2.31 0.406 -5.68 0.0000000135  0.0000459    68 Igkc  
6 ENSMUSG00000060586    5376.          -1.86 0.473 -3.92 0.0000871     0.0217       96 H2-Eb1

This was the depiction using as head(res)

ADD REPLY • link updated 2 hours ago by James W. MacDonald 67k • written 3 hours ago by Gordon • 0

score 0 · Answer 1 · 2024-10-22

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 28 minutes ago

United States

Oh. You used 'key' as the argument name when it's actually 'keys'. Also, those are Ensembl IDs, so you need to use 'ENSEMBL', not "ENTREZID".

ADD COMMENT • link 2 hours ago James W. MacDonald 67k