Statistic on FPKMs of gene in one condition

Renshin · 05-09-2016, 03:27 AM

Hello,

With the help of cufflinks; I calculated the number of FPKM for each contigs. In my study, I don't want to know which genes are expressed differently according to the conditions. I just want to know which ones are the most expressed. What program can I use or statistic?

Thank you for you help

dpryan · 05-09-2016, 06:45 AM

If you already have FPKMs then you already have your answer. The FPKM is the metric, just use the highest X%.

Renshin · 05-09-2016, 08:59 AM

I have perhaps statistically classify the FPKMs , it could be interesting. No ?

dpryan · 05-09-2016, 12:52 PM

You can use a method like zFPKM if you need something other than top X%, but that's not what you mentioned in your first post.

Renshin · 05-09-2016, 01:34 PM

Thank you, very interesting. I'm researching of ideas for my study on the FPKMs. I'm open to ideas.

Renshin · 05-12-2016, 09:23 AM

I calculated the zFPKM, but I don't calculate the treshold because I don't have a file containing the results of chromatin state analysis. Moreover, i work about an insect, i can't use threshold de -3 for human.

Can you help me

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05-09-2016, 03:27 AM	#1
Renshin Junior Member Location: Amiens Join Date: May 2016 Posts: 4	Statistic on FPKMs of gene in one condition Hello, With the help of cufflinks; I calculated the number of FPKM for each contigs. In my study, I don't want to know which genes are expressed differently according to the conditions. I just want to know which ones are the most expressed. What program can I use or statistic? Thank you for you help

05-09-2016, 06:45 AM	#2
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	If you already have FPKMs then you already have your answer. The FPKM is the metric, just use the highest X%.

05-09-2016, 08:59 AM	#3
Renshin Junior Member Location: Amiens Join Date: May 2016 Posts: 4	I have perhaps statistically classify the FPKMs , it could be interesting. No ?

05-09-2016, 12:52 PM	#4
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	You can use a method like zFPKM if you need something other than top X%, but that's not what you mentioned in your first post.

05-09-2016, 01:34 PM	#5
Renshin Junior Member Location: Amiens Join Date: May 2016 Posts: 4	Thank you, very interesting. I'm researching of ideas for my study on the FPKMs. I'm open to ideas.

05-12-2016, 09:23 AM	#6
Renshin Junior Member Location: Amiens Join Date: May 2016 Posts: 4	I calculated the zFPKM, but I don't calculate the treshold because I don't have a file containing the results of chromatin state analysis. Moreover, i work about an insect, i can't use threshold de -3 for human. Can you help me