Question

How to obtain gene symbols from the result list of GEO2R?

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5.0 years ago

Sib ▴ 60

It is an image of GEO2R results How can I obtain gene symbols of these gens by R or by online tools? (Maybe you say by online converters such as BioMart I can convert GB_ACC to gene symbol. But, the problem is that in the GB_ACC column there are different formats of IDs like NM_201591(a RefSeq ID), BX100997, BC043554 (a gene bank accession number) and NR_038236.)

rna-seq R • 4.9k views

ADD COMMENT • link updated 5.0 years ago by prince26121991 ▴ 70 • written 5.0 years ago by Sib ▴ 60

score 2 · Accepted Answer · 2019-12-10

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5.0 years ago

prince26121991 ▴ 70

Try this I think it will solve your issue Click on Select columns

SELECT column which you want to kept

ADD COMMENT • link 5.0 years ago by prince26121991 ▴ 70

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Thank you so much.

ADD REPLY • link 5.0 years ago by Sib ▴ 60

score 1 · Accepted Answer · 2019-12-10

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5.0 years ago

Devon Ryan 105k

There are Bioconductor packages for most common arrays. That one appears to be some sort of agilent array, so perhaps the MmAgilentDesign026655.db package is what you need.

ADD COMMENT • link 5.0 years ago by Devon Ryan 105k

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And after installing it, How should I use it?

ADD REPLY • link 5.0 years ago by Sib ▴ 60

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See the vignette for the package

ADD REPLY • link 5.0 years ago by Devon Ryan 105k

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You can use the Biomart in R. https://bioconductor.org/packages/release/bioc/html/biomaRt.html

ADD REPLY • link 5.0 years ago by skjobs ▴ 190