Map mouse RNA-seq Ensembl gene ids to "org.Mm.eg.db", but get some "UNKNOWN" gene symbol, like "NA..25729", is it normal?
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7 weeks ago
FantasticAI ▴ 60

Hi

I was trying to map mouse RNA-seq Ensembl gene ids to "org.Mm.eg.db" database, but get some "UNKNOWN" gene symbol, like "NA..25729", is it normal? How to explain it?

> tail(sigRes, 20)
log2 fold change (MLE): condition veh treated vs Normal 
Wald test p-value: condition veh treated vs Normal 
DataFrame with 20 rows and 6 columns
                  baseMean     log2FoldChange             lfcSE              stat               pvalue                 padj
                 <numeric>          <numeric>         <numeric>         <numeric>            <numeric>            <numeric>
NA..24549 105.664610578867 -0.770851759027846 0.233861917397644 -3.29618335300458 0.000980080281024346  0.00728504197472075
NA..24736 194.808838056677 -0.777760696534117 0.176163090877232 -4.41500369152888 1.01008266599123e-05 0.000184764180433743
NA..24742  51.487205963512 -0.736813603895114 0.276505705509743 -2.66473200810372  0.00770496973152258   0.0355406001475733
NA..24771 32.7124262550747 -0.833333429117127 0.247744784071624  -3.3636769881549 0.000769115030514744  0.00604242521145351
NA..25060 26.8845598681704 -0.838844475436016 0.324237832852246  -2.5871270729171  0.00967798937687407   0.0424060796355776
...                    ...                ...               ...               ...                  ...                  ...
NA..25733 76.7304148111874   1.81343359759673 0.301081645433979  6.02306259812965 1.71147210716138e-09 2.06118620535881e-07
NA..25734  66.482246397807  -1.00893704478236 0.294547565918586 -3.42537899315465 0.000613942349757262  0.00505885155328218
NA..26711 23.8857237355767  -1.87353864198739 0.359953640674784  -5.2049442769218 1.94054827255956e-07 8.02208794817031e-06
NA..26823 71.7313063347421 -0.746309692021764 0.191171179956943 -3.90388180995616 9.46620219766865e-05  0.00111428430953913
NA..27216 33.2338519038919 -0.716360871174029 0.225097752860465  -3.1824434587674  0.00146038026672219  0.00989818570499574
DEseq2 rna-seq DEG • 285 views
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Hi,

Can you please provide the code that you've used to perform that task?

Otherwise it makes it difficult to figure out how you did it and when (if) the problem happened.

António

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