Question: Persues analysis of single patient's T and N tissues
0
gravatar for BabySteps
5 weeks ago by
BabySteps0
BabySteps0 wrote:

This is about T vs N tissue from each patient...for my experiment I also need to do stat analysis for every paired T:N, instead of grouping them all together as T and N tissues for all the patients I have.

May I please ask how you do the stat analysis for this in Perseus or in Excel.

so far, i do get the intensities for each tumor and normal tissue, get their log 2 values and perform ttest with the data...then the results always give me no significance difference at p=0.05.

may you please assist me on this. thank you so much.

gene • 117 views
ADD COMMENTlink modified 5 weeks ago by szymanski.wit20 • written 5 weeks ago by BabySteps0
1
gravatar for szymanski.wit
5 weeks ago by
szymanski.wit20 wrote:

You should get the rations of T/N for each pair and then proceed with the data like with the SILAC dataset. Check here: https://www.zmbh.uni-heidelberg.de/Central_Services/Mass_Spectrometry/PDF/150206%20Perseus%201.5.1.5%20Tutorial_Version2.pdf

In short. when you have ratios for different replicates, you should perform One-sample test, which is an option in Perseus.

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by szymanski.wit20

thank you for your attention. I will try that now.

Sent with warn regards,

Tess Cation

ADD REPLYlink written 5 weeks ago by BabySteps0

Dear Zymanski,

Good day!

may i have some follow up questions

I checked the examples in the link and im confused which data i begin wiith, please help.

i have the following data from my ms data raw files, and im confused which one to use for the perseus analysis

126 and 131 are internal standards 127, 128, 129, 130 Normal adjacent tissues 127,128, 129, 130 Tumor tissues

I want to study each patient, for example patient 127 first.

here a screen shot of the data i got after proteome discoverer run.

[image: image.png]

thank you so much in advance.

Sent with warn regards,

Tess Cation

ADD REPLYlink written 5 weeks ago by BabySteps0
1

You want to study each patient separately? Because without any replications, replicates etc. Perseus will not give you any meaningful p-values. If you take all T samples and all N samples, then you have 4 replicates and then Perseus will provide you p-values.

If you want to study each patient separately, then you can just calculate the T/N ratio and take a look at the ones that are changing the most.

Try also finding help here: https://groups.google.com/forum/#!forum/perseus-list

Greets

ADD REPLYlink written 5 weeks ago by szymanski.wit20

Thank you so much for your kind assistance.

I really appreciate your help.

More power!

ADD REPLYlink written 5 weeks ago by BabySteps0
1

Power to the people

ADD REPLYlink written 5 weeks ago by Kevin Blighe47k
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