GREAT VIDEO.... can u please guide how to give custom color to data point in X axis .. like if we want to give different color to x 2 and x>5 and logFC >2 ..... ?????? how to do this ?
Hi there, really useful tutorial thank you! However, I was wondering if there is a way that I can also easily highlight below and above a log(fold change) threshold (i.e -1 to 1) as well as having a threshold on the Y-axis?
Hi Sam. Thanks for the feedback. Hmm, so you also want to highlight that genes that are above a fold change threshold too. I think if you sort your results in Excel beforehand in fold change order then it may be possible. Then in GraphPad you will have to manually select and change the colour of the data points that are >1 fold change and >-1 fold change. However, I don't think it will be straight forward as you will also need to ensure they are above your FDR threshold too so that the colours make sense. Does that help? Essentially, try and sort your data in Excel before importing into GraphPad to identify the genes you want to highlight (change colour)
Hi thank you so much and is really useful tutorial but hope another tutorial how to do a log(fold change) nd -log(false discovery rate ) of RNA-seq for comparing 6 patients (paired) before and after surgery? Looked forward to hear from you
Thanks to you good education. I have 1 question. is there any way to draw line from specific target gene such as Slc25a1 in your video. I want to make a draw line and emphasis on my specific genes
that's so useful! thank you. I have a question about the legend of that graph, is there any possibility of creating a legend that will be connected to the color of the dots? I mean to write "upregulated" or "downregulated"
@@muktabasu6405 ah sorry I got confused with previous Prism versions. According to Prism the there is no limit on the number of rows. So it should be possible yes. But i found my software was slow when i had a large dataset open. Just something to remember
JOIN THE GRAPHING WITH GRAPHPAD PRISM FREE ONLINE COURSE
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What is difference between LSD value p < 0.05 and FDR? Kindly make a video on FDR
GREAT VIDEO.... can u please guide how to give custom color to data point in X axis .. like if we want to give different color to x 2 and x>5 and logFC >2 ..... ?????? how to do this ?
Thanks a ton!
Note: FDR < 0.01 so -log (0.01) = 2 which is the threshold
People have already said this but this is really such a good tutorial. Thanks for the help.
thank god i found your video, my life is saved again ㅠㅠ
WOW this was extremely useful and so easy to follow! thank you very much
neat and clean explanation..no confusing terms...thanks
Hi there, really useful tutorial thank you! However, I was wondering if there is a way that I can also easily highlight below and above a log(fold change) threshold (i.e -1 to 1) as well as having a threshold on the Y-axis?
Hi Sam. Thanks for the feedback. Hmm, so you also want to highlight that genes that are above a fold change threshold too. I think if you sort your results in Excel beforehand in fold change order then it may be possible. Then in GraphPad you will have to manually select and change the colour of the data points that are >1 fold change and >-1 fold change. However, I don't think it will be straight forward as you will also need to ensure they are above your FDR threshold too so that the colours make sense. Does that help? Essentially, try and sort your data in Excel before importing into GraphPad to identify the genes you want to highlight (change colour)
Thanks a lot. Was immensely clear and useful.
Thanks for your feedback and support
So easy to understand. Thank you soooo much
Very welcome
How to show upregulated and downregulated genes in two different colors (red and blue) rather than showing both in single color?
Hi thank you so much and is really useful tutorial but hope another tutorial how to do a log(fold change) nd -log(false discovery rate ) of RNA-seq for comparing 6 patients (paired) before and after surgery? Looked forward to hear from you
How did you calculate the log ten .. is it the log of the median ?
Can I follow the same steps in the video but using "-log10(adjusted p-value) and the log2(FC)"?
This is a great tutorial and extremely useful! Thanks!
Well done Sir. A beautiful video. Very informative !!!
Thank you kindly!
Really clear video - thank you
Thanks to you good education. I have 1 question. is there any way to draw line from specific target gene such as Slc25a1 in your video. I want to make a draw line and emphasis on my specific genes
Great tutorial. Explained nicely
Very nice tutorial!
when row titles (gene names) are crammed, is there any option to draw lines connecting dots and row titles?
This was extremely helpful. Thank you!
Please keep this type of content going! This is such a time saver THANK YOU =D
that's so useful! thank you. I have a question about the legend of that graph, is there any possibility of creating a legend that will be connected to the color of the dots? I mean to write "upregulated" or "downregulated"
Very useful!! Thank you very much!!!!!
Thank you max. You save my life !
You are welcome :)
Thanks a lot..very good content.
Thanks for the kind feedback
Thank you so much. It's clear !
Thank you so much. It is a great tutorial like always.😊
Thank you Tyrant :)
is it log or log base 2
Thank you so much!
many many thanks!!!!!!!
Perfect. Thanks
This is so helpful!!
Awesome!! Thanks
Great tutorial, thanks a lot
You are welcome
very helpful. Thank you very much !!!!!
Thank you Anne :)
Do graph pad also plots more than 50k genes??
I believe the limit in Prism is 10,000 rows per dataset, so that would not be possible. It may be worth using R to do that
Bt you used a dataset which u mentioned had 15k genes..
@@muktabasu6405 ah sorry I got confused with previous Prism versions. According to Prism the there is no limit on the number of rows. So it should be possible yes. But i found my software was slow when i had a large dataset open. Just something to remember
Thank you very much.. i am trying it now. Hopefully, i will succeed