@asifmolbio Okay Thank you. Here you have mentioned that, it is applicable for 15 samples. Samples means control and treatment plant numbers? Or something else! Cause I have one control and 2 treatments. Can I do WGCNA with these?
@asifmolbio Okay got it. Your videos are too helpful brother. I watch your videos and the explanation is better than other videos. I am in Zhengzhou University, Henan, China, doing PhD with Agriculture field. Could you please share your wechat?
Hi sir this is very usefull video , My question is if i have microarray data specially expression profiling by array and i want to perform WGNCA analysis can i able to performe with idep server ? If yes kindly help me on this
Sir,where s ur institute, want to come and learn especially R,python,WGCNA, Deseq2,Roc, PCA .Practical ly i want to learn ,m doing phd in bioinformatics without nothing,Can u pls help me .
I am performing iDEP with gene ids of wheat. But on loading data in iDEP it shows disconnected from the server. Please provide any suggestion to resolve the problem.
Dear sir, i want to verify some genes of my interest are co-expressed or not via this iDEP tool. Is it possible, is their any need of special R coding If I want to check specific genes are responsible for specific hormonal pathway. can I do it via this iDEP tool? ( If the RNA SEQ data is not available in iDEV itself) Thank you in advanced
Sir, I have been following your videos from last one year. I have learned a lot of things from your videos. Sir, can u make a video about how to apply WGCNA in microarray dataset using R? Please sir, I will be very grateful if you make a video on this topic. I have been trying to perform WGCNA in GSE62232 but I am failing.
Hi Dr Asif. You said atleast 15 samples. So, is it total 15 samples taking all groups or each group should have 15 samples? Also do you have a video where you have prepared the gene count file from RNA-Seq sample data?
This is really amazing and easy explanation. I will do this type of analysis in near future. and refer to your video
Glad if it’s helping
Very informative lecture
Glad you like it
How do I get the Design file of the specific gene ID?
Need to create by yourself see the video on my channel to learn
Thanks for sharing this video you kinda saved me
I still have question, what is the edge threshold
thank you^^^^^^^
Welcome you can start by setting it to 0.5 as a starting point.
Hello brother, is it only for Arabidopsis or I can use other plant ids?
Any specie is okay
@asifmolbio Okay Thank you. Here you have mentioned that, it is applicable for 15 samples. Samples means control and treatment plant numbers? Or something else! Cause I have one control and 2 treatments. Can I do WGCNA with these?
@@tanusreedatta4493 total including control, treatment and replicates should be more than 15
@asifmolbio Okay got it. Your videos are too helpful brother. I watch your videos and the explanation is better than other videos. I am in Zhengzhou University, Henan, China, doing PhD with Agriculture field. Could you please share your wechat?
@asifmolbio Thank you brother
sir what is soft and edge threshold
Soft thresholding retains all connections and scales their importance, while edge thresholding keeps only strong connections and eliminates weak ones.
sir tutorial nicely explained but please explain the theory bit more in detail
@@sreeram6416 this analysis is about performing WGCNA analysis
@@sreeram6416 for interpretation i will record separate
Hi sir this is very usefull video , My question is if i have microarray data specially expression profiling by array and i want to perform WGNCA analysis can i able to performe with idep server ? If yes kindly help me on this
Yes, you can
@@asifmolbio sir how to do that sir can u please explain me
upload your expression file in excel similar to i have done in this video
@@asifmolbio only expression file is enough ???? no need of design file??
let me send you a design file video
Sir,where s ur institute, want to come and learn especially R,python,WGCNA, Deseq2,Roc, PCA .Practical ly i want to learn ,m doing phd in bioinformatics without nothing,Can u pls help me .
I am based in china at present. One to one session can be booked: if needed go to about section on TH-cam channel and fill the form
Where will I get the link and fill the form ji
www.youtube.com/@asifmolbio/about
I am performing iDEP with gene ids of wheat.
But on loading data in iDEP it shows disconnected from the server. Please provide any suggestion to resolve the problem.
I never faced any problem like this. Probably website will be under maintenance you can try after a day or two.
@@asifmolbio Okk sir
Any alternative to do WGCNA
Alternative is through R programming. But i am sure, website will be functional. You can try after changing internet or computer
@@asifmolbio okk sir
check your input data whether it is in correct format. may i know how many samples you have given as input.
Dear sir, i want to verify some genes of my interest are co-expressed or not via this iDEP tool. Is it possible, is their any need of special R coding
If I want to check specific genes are responsible for specific hormonal pathway. can I do it via this iDEP tool? ( If the RNA SEQ data is not available in iDEV itself)
Thank you in advanced
There is no tool to verify to find genes co expressing.
You need to look your pathway by yourself from all pathways
Watch this video to get an idea
How to select genes for qPCR validation in transcriptome/RNA seq data?
th-cam.com/video/PRhHBcjKAKU/w-d-xo.html
one more question 🙋 which step can I set the p.value to 0.05? THANK YOU^^
In the iDEP tool
In the start of analysis
Sir, I have been following your videos from last one year. I have learned a lot of things from your videos. Sir, can u make a video about how to apply WGCNA in microarray dataset using R? Please sir, I will be very grateful if you make a video on this topic. I have been trying to perform WGCNA in GSE62232 but I am failing.
Thank Sakib, Sure i have noted down your topic, i will make a video soon inshaAlllah.
@@asifmolbio Thank you so much sir.
@@asifmolbio sir can we expect the video near future? Plz sir
If sample size is less then 15 then what we should do?
Then authentication of wgcna can be questionable to some extent.
Good afternoon sir
I am using list of wheat gene ids with TraesCS4D02G203800 but iDEP showing error I'd not recognised.
What I have to do sir?
Can you change the gene and try any other id ? Still same
Hi Dr Asif. You said atleast 15 samples. So, is it total 15 samples taking all groups or each group should have 15 samples? Also do you have a video where you have prepared the gene count file from RNA-Seq sample data?
All the samples from all groups should be more than 15, not from one group
How to calculate FC, log2FC, Pvalue, Padj, Up/down genes in RNA seq data using Excel
th-cam.com/video/HH3Mll4W5WE/w-d-xo.html
design file is the metadata file know sir
Design file is for choosing treatments comparisons