Question

How can I create ChipDb for Solanum lycopersicum?

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knishida ▴ 20

@knishida-8230

Last seen 4.8 years ago

United States

Hi

I would like to create ChipDb package for Solanum lycopersicum.

It seems there is already Solanum lycopersicum OrgDb in AnntationHub.

And I have an ID mapping table for my probeIDs and ENTREZ IDs.

I think makeDBPackage creates sqlite database from such a table.

makeDBPackage needs schema for the argument, but there is no available dbschema for Solanum lycopersicum.

How can I create ChipDb for Solanum lycopersicum?

annotation • 1.1k views

ADD COMMENT • link updated 9.2 years ago by James W. MacDonald 67k • written 9.2 years ago by knishida ▴ 20

score 4 · Accepted Answer · 2015-09-10

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 6 hours ago

United States

You use makeChipPackage() from AnnotationForge, which will determine the correct schema (in this case the NOCHIPSCHEMA_DB) automatically.

ADD COMMENT • link 9.2 years ago James W. MacDonald 67k

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Thanks James.

makeChipPackage()

almost works well.

But I could NOT find the way to assign multiple ENTREZ IDs for a probe ID.

It seems ChipDb has is_multiple column and the value is 1 when the probe ID has multiple ENTREZ IDs.

How can I assign multiple ENTREZ IDs for a probe ID ?

ADD REPLY • link 9.2 years ago knishida ▴ 20

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It's as simple as you might expect. You put the probe ID in twice (on two different lines).

ProbeID_X   12345
ProbeID_X    45322

ADD REPLY • link 9.2 years ago James W. MacDonald 67k

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Thanks again James!

It works well!.

Now I have added the is_multiple 1 column to my db.

ADD REPLY • link 9.2 years ago knishida ▴ 20