Need help in running GO analysis
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Rishav ▴ 20
@rishav-25031
Last seen 3 days ago
Patna

Hello everyone. I am trying to do GO analysis but I am getting an error. Please help me to sort out that problem. These are the codes that I have been using

#head(resOrdered)
                baseMean log2FoldChange     lfcSE      stat      pvalue
                <numeric>      <numeric> <numeric> <numeric>   <numeric>
ENSG00000185559 2060.9630       -7.90823  1.101221  -7.18132 6.90399e-13
ENSG00000167244 3949.7195       -5.08718  0.754385  -6.74347 1.54643e-11
ENSG00000149948  321.4033       -6.05676  0.947898  -6.38967 1.66246e-10
ENSG00000225972 1293.5730        3.62415  0.592158   6.12024 9.34374e-10
ENSG00000002726   56.1686       -3.15318  0.527678  -5.97558 2.29276e-09
ENSG00000207805   10.6401       -4.28120  0.792715  -5.40068 6.63898e-08
                       padj
                  <numeric>
ENSG00000185559 2.10979e-08
ENSG00000167244 2.36286e-07
ENSG00000149948 1.69343e-06
ENSG00000225972 7.13838e-06
ENSG00000002726 1.40129e-05
ENSG00000207805 3.38134e-04


# universe <- rownames(resOrdered)
# library(org.Hs.eg.db)
# genemap <- select(org.Hs.eg.db, selected, "ENTREZID", "SYMBOL")
Error in .testForValidKeys(x, keys, keytype, fks) : 
  None of the keys entered are valid keys for 'SYMBOL'. Please use the keys method to see a listing of valid arguments.
RNASeq R • 196 views
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 selected <- rownames(sig)
selected
 [1] "ENSG00000185559" "ENSG00000167244" "ENSG00000149948" "ENSG00000225972"
 [5] "ENSG00000002726" "ENSG00000207805" "ENSG00000213759" "ENSG00000225431"
 [9] "ENSG00000146755" "ENSG00000081051" "ENSG00000268916" "ENSG00000226674"
[13] "ENSG00000240280" "ENSG00000260468" "ENSG00000144407" "ENSG00000224271"
[17] "ENSG00000266976" "ENSG00000124333" "ENSG00000108849" "ENSG00000137434"
[21] "ENSG00000214814" "ENSG00000116017" "ENSG00000176566" "ENSG00000184368"
[25] "ENSG00000112164" "ENSG00000171004" "ENSG00000187922" "ENSG00000272620"
[29] "ENSG00000144045" "ENSG00000236254" "ENSG00000251775" "ENSG00000251199"
[33] "ENSG00000073792" "ENSG00000275325" "ENSG00000158639" "ENSG00000233797"
[37] "ENSG00000268460"
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The above code could be like :

genemap <- select(org.Hs.eg.db, selected, "ENTREZID", "ENSEMBL")
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@kevin
Last seen 2 hours ago
Naas, Republic of Ireland

Hi, sometimes it's better to write out the parameter names in full, to leave no doubt about 'what is being used where'.

Your 'keys' are Ensembl [human] gene IDs. Therefore, your 'keytype' must be ENSEMBL.

These will work for you:

require(org.Hs.eg.db)

mapIds(
  org.Hs.eg.db,
  keys = selected,
  column = 'SYMBOL',
  keytype = 'ENSEMBL')

select(
  org.Hs.eg.db,
  keys = selected,
  column = c('SYMBOL', 'ENTREZID', 'ENSEMBL'),
  keytype = 'ENSEMBL')

Kevin

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Yes, I already solved that problem. I understand what was the problem .

Thank you so much for your time

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