Question

Need help in running GO analysis

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Rishav ▴ 20

@rishav-25031

Last seen 21 months 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 • 1.3k views

ADD COMMENT • link 3.6 years ago Rishav ▴ 20

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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"

ADD REPLY • link 3.6 years ago Rishav ▴ 20

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The above code could be like :

genemap <- select(org.Hs.eg.db, selected, "ENTREZID", "ENSEMBL")

ADD REPLY • link 3.6 years ago Rishav ▴ 20

score 1 · Answer 1 · 2021-05-09

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Kevin Blighe ★ 4.0k

@kevin

Last seen 26 days ago

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

ADD COMMENT • link 3.6 years ago Kevin Blighe ★ 4.0k

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

Thank you so much for your time

ADD REPLY • link 3.6 years ago Rishav ▴ 20