Question

single probe represent multiple genes?

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mathavanbioinfo ▴ 20

@mathavanbioinfo-11955

Last seen 7 months ago

India

Hello friends

I am doing micro array data analysis(HGU1333plus2), i got the expression matrix file by using gcrma , but the some probe is represent multiple gene like this . how can we treat this, then some probe is not matched it shows NA can delete it , next i take this file for analyze WGCNA , please share your knowledge ,

221251_x_at	1	221251_x_at	INO80B /// INO80B-WBP1	NA
65133_i_at	1	65133_i_at	INO80B /// INO80B-WBP1	NA
223072_s_at	1	223072_s_at	INO80B /// INO80B-WBP1 /// WBP1	NA
1559716_at	1	1559716_at	INO80C	INO80C
229582_at	1	229582_at	INO80C	INO80C
220165_at	1	220165_at	INO80D	INO80D
226555_at	1	226555_at	INO80D	INO80D

gcrma microarray expressionset • 1.4k views

ADD COMMENT • link updated 7.8 years ago by svlachavas ▴ 840 • written 7.8 years ago by mathavanbioinfo ▴ 20

score 0 · Answer 1 · 2017-02-10

Dear Mathavanbioinfo,

i think you have asked the same question in a recent previous post that it has been already answered:

How to combine multiple probes representing a single gene?

Also, some suggestions about preprocessing with WGCNA can be found here:

https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html

Best,

Efstathios