single probe represent multiple genes?
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@mathavanbioinfo-11955
Last seen 14 months ago

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 • 727 views
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svlachavas ▴ 780
@svlachavas-7225
Last seen 2 days ago
Germany/Heidelberg/German Cancer Resear…

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

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