Question

weird to see top gene mutation frequency on my dashboard (plotmafSummary(maf))

0

Entering edit mode

4.3 years ago

gaom001 ▴ 10

Is there anyone knows what is going on here? Never saw this before.

enter image description here

R maf • 1.1k views

ADD COMMENT • link updated 4.3 years ago by h.mon 35k • written 4.3 years ago by gaom001 ▴ 10

1

Entering edit mode

What is odd here? That all frequencies are 67%? That all bars have the same length, even if they all have the same frequency of 67%? Please be considerate and provide more details and background.

You either missed a deadline at March, 4, or Excel mangled some gene names - I guess the later occurred. See Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics and Gene name errors are widespread in the scientific literature for background on the problem. You can try to fix the gene names with Truke, a web tool to check for and handle excel misidentified gene symbols. The latest funny (and sad) development on this issue is Scientists rename human genes to stop Microsoft Excel from misreading them as dates.

ADD REPLY • link 4.3 years ago by h.mon 35k

0

Entering edit mode

Yes, they have same percentage, but the top gene bar length is longer than others which have same percentage. I tried more samples today, and it did show again. It is very weried, but I found one gene called 4-Mar in my csv file. lol...

Thank you again.

ADD REPLY • link 4.3 years ago by gaom001 ▴ 10

0

Entering edit mode

enter image description here

ADD REPLY • link 4.3 years ago by gaom001 ▴ 10

score 2 · Answer 1 · 2020-08-08

2

Entering edit mode

4.3 years ago

Kevin Blighe 88k

Your sample number could be low.

ADD COMMENT • link 4.3 years ago by Kevin Blighe 88k

1

Entering edit mode

You are right, I only have 3 samples. I tried more samples today, and I did not see this odd again. The length of the top gene bar is same as others for more samples.

ADD REPLY • link 4.3 years ago by gaom001 ▴ 10