Hi, very nice video and explanation. When I calculate FC I get -Inf values as there are 0 values in my data , so could you please let me know how can I overcome this?
@asifmolbio
Жыл бұрын
Thanks ankola, You can search all zeros and delete those rows
@naveenkudupudi
5 ай бұрын
Thank you for doing this. Just enough detail to understand and do further research.
@asifmolbio
5 ай бұрын
Glad if its helpful
@elliealy4603
Ай бұрын
Assalam Alaikum Sir, Please the Benjamini web doesn't work, could you suggest another web or other method to know significant and non-significat?
@asifmolbio
Ай бұрын
Wslam what’s the error
@elliealy4603
Ай бұрын
@@asifmolbio The FDR correction online website doesn't work, so i couldn't do the significant and non-significant part
@asifmolbio
Ай бұрын
Try again later may be there is server issues
@dr.mohdaamir6688
Жыл бұрын
How to decide our data is one tailed or two tailed test ??
@asifmolbio
Жыл бұрын
Two tailed: Give possibility to see difference on both side at a time (up and down), when you are not sure, which to use, its always better to use two tailed test. (You can also use two tailed when anyone can be control) One tailed: give possibility to see difference on one side (up or down) only at a time. It is more stringent. (You can also use one tailed when control is already known) For more details you can watch related videos on KZitem.
@asifmolbio
Жыл бұрын
kzitem.info/news/bejne/ymhpwKqffHuVe6w
@dr.mohdaamir6688
Жыл бұрын
@@asifmolbio Thank You so much
@BilalRaza-qz7dc
3 ай бұрын
Hello Can you tell me if i have three groups how i can find FC value
@asifmolbio
3 ай бұрын
Take average and follow average
@jobsworld99
3 ай бұрын
but you are divided one group to other to find FC value when 3 groups how we will devide..for example i have control, carbon and combine group with each have3 treatments@@asifmolbio
@Yhusi
6 ай бұрын
Thanks so much for the detail explanation. If I only want to know the amount expression level of 1 gen in only the control group, should I normalized (devide) with internal control/house keeping gene (like when we calculate in the qPCR analysis)? Should I also log2 it first or use the raw read data? Thank you
@asifmolbio
6 ай бұрын
If you have internal control then you can normalize it with that
@Su.arya31
6 ай бұрын
Hello sir in geo it is given logFC value , how can we convert to normal fold change value?
@asifmolbio
6 ай бұрын
To convert a logFC (logarithm of fold change) value to a FC (fold change) value in Excel, you can use the formula: =10^(A1) Assuming your logFC value is in cell A1, this formula will return the FC value. Just replace A1 with the cell reference containing your logFC value.
@Su.arya31
6 ай бұрын
Sir thank you for your response , just want to know the given value logFC from database are log base 10 or log base2?
@asifmolbio
6 ай бұрын
Base 10
@hendadel8042
10 ай бұрын
Hi sir. I have data with only 4 subtypes diseases for TNBC, with out normal tissues, How can I do my RNA-Seq analysis?
@asifmolbio
10 ай бұрын
Infact always should have a control for comparison. Now you can consider one sub type as control for comparison
@samysolano8526
Жыл бұрын
Thanks for the video. If I don't have a control group in my experiment and I did ddCt with the difference between my dCt sample value - the highest dCt value in all the samples, what should I use in the first array of the T- test? Thanks
@asifmolbio
Жыл бұрын
You can use housekeeping gene CT values as control
@vahinireddy3707
Жыл бұрын
Hi sir , thanks for the video! Can we calculate Pcal from fold change values and also what is the difference between Pcal and padj
@asifmolbio
Жыл бұрын
If we comparison then we can calculate p value
@dr.mohdaamir6688
Жыл бұрын
Is there any windows based tool to calculate KEGG based Rich factor analysis in IDEP they are not filtering based on Rich factor
@asifmolbio
Жыл бұрын
I think then you need to do it with R. I need to search for online web-based tool, if i got it i will let you know.
@dr.mohdaamir6688
Жыл бұрын
@@asifmolbio ok thanks
@okoseimiemaibifubara2080
7 күн бұрын
Thank you for a wonderful explanation, please is the control our reference gene while treatment our target gene. Thank You
@asifmolbio
7 күн бұрын
@@okoseimiemaibifubara2080 thanks, no control is a separate treatment.
@okoseimiemaibifubara2080
7 күн бұрын
In my analysis, I used the reference gene and my genes of target is GH and IGF-1 with eight diets. How do I arrange it, please
@asifmolbio
7 күн бұрын
@@okoseimiemaibifubara2080 follow like i have arranged and shown in example. In your case each Treatment (8 in your case ) will be compared with control separately.
@okoseimiemaibifubara2080
7 күн бұрын
Please where is your reference gene in the arrangement, Thank you
@asifmolbio
7 күн бұрын
@@okoseimiemaibifubara2080 this data is from transcriptome let me give you a link of qPCR data.
@Sneha_294
10 ай бұрын
If the control group has some values and the treated cells has 0 as a value, then how can we identify the downregulated genes? For example, my control groups shows 23, 32, 29 as their read count value. In my treated group all the samples are showing 0. So when I calculate the fold change treated/ control, the fold change is changing to 0. Can you tell me how can we resolve this?
@asifmolbio
10 ай бұрын
You should take the value of treated group as 1 for zero. Hopefully will solve the problem
@Sneha_294
10 ай бұрын
@@asifmolbio Thank you. Recently binge watching your videos. Very useful!!
@asifmolbio
10 ай бұрын
Thats great 😊
@aqaikalanhassanyar305
Жыл бұрын
I would like to know when we want to plot the fpkm treated vs control which fpkm should be used in the grsphs?
@asifmolbio
Жыл бұрын
Take average of all three, and represent it as mean of expression and then can be shown in the form of graphs
@elMARABIYOCHO1989
Жыл бұрын
Hi. Why did you go for a one-tailed test instead of the two-tailed test? Aren't you trying to see if the genes are upregulated or downregulated? Thanks in advance.
@asifmolbio
Жыл бұрын
Two tailed test can also be used if possibility on both side, but i was focusing on only one side
@elMARABIYOCHO1989
Жыл бұрын
thank you so much.@@asifmolbio
@nwislamicschool
Жыл бұрын
Excellent Video and you have explained it in such a simplistic manner. My question is if I have Gene expression data on 730 genes in 50 mice with one cancer and 50 mice as control. Can I use this same analogy to determine the significant and non-significant genes based on log 2 data of 50 readings in each group? Highly appreciate your time to respond,
@asifmolbio
Жыл бұрын
Yes you can butWhat you mean by 50 readings? Replicates
@nwislamicschool
Жыл бұрын
@@asifmolbio Sorry; should have been more clear ; I meant 50 samples
@asifmolbio
Жыл бұрын
Yes you can
@dr.mohdaamir6688
Жыл бұрын
I need to convert Gene ID to Gene ontology number. Kindly suggest any direct method to convert or suggest some tools.
@asifmolbio
Жыл бұрын
which specie are working with?
@dr.mohdaamir6688
Жыл бұрын
@@asifmolbio tomato (Solanum lycopersicum L.)
@nidaajmal5613
Жыл бұрын
Hi, this video helped a lot! could you please let me know if there are any databases available online that help in identifying the signaling pathway of the genes that will be filtered out from RNA seq data?
@asifmolbio
Жыл бұрын
As such there is no database to identify signalling pathway genes but there are tools which can filter genes and map them to their databases. On my channel you can see video about iDEP RNA seq tool and GO Shiny tool.
@nidaajmal5613
Жыл бұрын
@@asifmolbio Thanks I will watch that. There are some tools available for identifying Kegg pathways, like DAVID gene bioinformatic tools, and path Visio, that I found so far.
@juli1
Жыл бұрын
Hello, I found that Qiagen Ingenuity Pathway Analysis (IPA) can help you to do so but it's not free. You can search for a free alternative, I'm sure that exists.
@aguscmzz
Ай бұрын
Hi Asif, why do you use paired data t student test? Are the treatments applied to the same individuals that were control before? I am trying to use these methology in another kind of study but I need to be sure in this aspect. Because we have not paired data, measures in controls and treatments are taken in different samples.
@asifmolbio
Ай бұрын
Hi, it sounds like you're exploring the use of a paired t-test but are concerned about its applicability to your study. The paired t-test is typically used when the same subjects are measured before and after a treatment, or when measurements are taken under two different conditions on the same individuals. This allows for controlling individual variability, making it easier to detect the effect of the treatment. However, since your controls and treatments are measured on different samples (i.e., they are not paired), the paired t-test wouldn't be appropriate. Instead, you'd want to use an independent samples t-test, which compares the means of two independent groups to see if there is a statistically significant difference between them. So, to summarize: - **Paired t-test:** Use when the same subjects are measured twice (e.g., before and after treatment). - **Independent samples t-test:** Use when comparing two different groups (e.g., control vs. treatment) with no pairing between them. Feel free to reach out if you need more clarification!
@aguscmzz
Ай бұрын
@@asifmolbio Ok, in my case, I could not use the paired option. I repeated the exercise in excell and all the values obtained are the same but also the FDR. If you try to make again, the values obtained for padjust are now differtents in the web... this implies that only two variables are now significants. Can you imagine why it occurs??? I can not...
@asifmolbio
Ай бұрын
Some FDR or p-adjust calculations might include a random component (e.g., in bootstrapping or permutations), especially in certain tools. This could result in slightly different results each time the analysis is run.
@karanvirkaushal8386
6 ай бұрын
Amazing video! So grateful to you sir...
@asifmolbio
6 ай бұрын
My pleasure
@toniromeroconde7193
8 ай бұрын
Hi Dr. Asif, If we take into account the FC values to see if there is an up or down regulation. What is the purpose of calculating log2FC?
@asifmolbio
8 ай бұрын
Taking the log2 fold change (log2FC) is a common practice in statistical analysis, especially in the context of gene expression data. The log2FC is preferred over the raw fold change (FC) for several reasons: 1. Symmetry: Log transformation makes the fold change symmetric around zero, which simplifies interpretation and statistical analysis. 2. Linear Scale: The log2FC brings the fold change to a linear scale, making it easier to work with in mathematical calculations and statistical models. 3. Stabilization: Log transformation stabilizes variance, helping to satisfy assumptions of normality in many statistical methods. 4. Biological Interpretation: Log2FC is more interpretable in a biological context. For example, a log2FC of 1 means a two-fold change, and a log2FC of 2 means a four-fold change. By using log2FC, researchers enhance the utility of gene expression data for analysis and interpretation, making it a standard practice in bioinformatics and genomics.
@m.awaisahmed8556
7 ай бұрын
How we can determined either which gene is down or upregulated in case we have more than 2 treatments in Gene expression anlysis ?
@asifmolbio
7 ай бұрын
Take an average of all treatments and compare treatment with control one by one
@m.awaisahmed8556
7 ай бұрын
@@asifmolbio Thanks Sir .
@asifmolbio
6 ай бұрын
Welcome
@muhammadwaqasluqman2977
11 ай бұрын
Thank yiu so much for this video.❤❤
@asifmolbio
11 ай бұрын
Glad you like it
@asktayyabrehman
Жыл бұрын
Thank you sir.
@asifmolbio
Жыл бұрын
Thanks
@Mr-Ejaz
8 ай бұрын
hello sir i want to contact you
@asifmolbio
8 ай бұрын
Please do an email to asifalikalas@foxmail.com
@Islamicvideos-2666
Жыл бұрын
Well done dr sahb
@asifmolbio
Жыл бұрын
Glad you like it
@natureabioros8686
Жыл бұрын
Fantastic tutorial. Logically organized and concise!
@asifmolbio
Жыл бұрын
Glad you like it
@hebanazir4970
8 ай бұрын
P value give me negative number in calculation
@asifmolbio
8 ай бұрын
Then its significant
@ritziroy148
Жыл бұрын
Thank you so much! This is so helpful.
@asifmolbio
Жыл бұрын
Glad if its helpful
@syamsidahrahmawati5974
Жыл бұрын
Thank you very much sir, very clear
@asifmolbio
Жыл бұрын
You are welcome
@Noor-sr5mj
11 ай бұрын
please give some practice material
@asifmolbio
11 ай бұрын
Sure will upload
@sharonhillary7783
7 ай бұрын
This video is beyond helpful, even for someone who does not understand excel, thanks a lot sir
@asifmolbio
7 ай бұрын
Glad if it’s helping
@BaNa2C2
11 ай бұрын
Hi Dr. Asif. Can I know is it okay to set upregulated genes as log2 fold change > 0 and downregulated genes as log2 fold change < 0 ?. I realized most papers use log2 fold change > 1 for upregulated genes and log2 fold change < -1 for downregulated genes . Only few papers set upregulated as log2 fold change > 0 and downregulated as log2 fold change < 0. Thank you
@asifmolbio
11 ай бұрын
if you will take logFC >0, it will be still okay. but as you know the level is too low so data would not be much meaningful. So its better if you take FC>1 atleast, would be best if you take FC>2.
@BaNa2C2
11 ай бұрын
@@asifmolbio thank you so much Dr.Asif
@BaNa2C2
11 ай бұрын
@@asifmolbio another question is if take FC>1 for upregulated then remaining FC1. Is this meant value below 1 to -1 e.g: 0.7, - 0.93 are not included?
@asifmolbio
11 ай бұрын
Yes right
@Beautifullife7189
3 ай бұрын
Thank you sir ,very helpful video ,
@asifmolbio
3 ай бұрын
Glad you like it
@najlaeel8217
4 ай бұрын
THANK YOU !
@asifmolbio
4 ай бұрын
You're welcome!
@MuhammadFaizan-mi9yo
Жыл бұрын
Can you please start a series of videos based on your previous research paper methodology, especially bioinformatics that one would learn strategies of research.and modern bioinformatics tecniques.
@asifmolbio
Жыл бұрын
Sure , Don’t forget to check playlists on my channel. Most of the relevant videos are already uploaded.
@MuhammadFaizan-mi9yo
Жыл бұрын
@@asifmolbio appricaited sir.
@MuhammadFaizan-mi9yo
Жыл бұрын
@@asifmolbioAoa sir how are you? xan you please suggest some paraphrasing and writing tools for Ph.D.? thesis writing paraphrasing,?
@partha_plethorapedia
11 ай бұрын
wonderful
@asifmolbio
11 ай бұрын
Glad you like it
@EdehAbigael
8 ай бұрын
This is very helpful. Thank you
@asifmolbio
8 ай бұрын
Glad if its helpful
@sangitapaul6463
Жыл бұрын
May I use this same method to analyze the proteomics data?
@asifmolbio
Жыл бұрын
Yes off course
@sangitapaul6463
Жыл бұрын
Thank you for your well explained video Sir
@sangitapaul6463
Жыл бұрын
Is it possible to do volcano plots with excel?
@asifmolbio
Жыл бұрын
@@sangitapaul6463 i will upload a video about volcano soon. Its possible by SR website, not by excel
@mitrabinda1992
4 ай бұрын
I really appreciate this channel and your quick responses on doubts.. being a beginner, I want to ask that, what are those values from which FC is calculated..
@asifmolbio
4 ай бұрын
Thanks, expression value
@mitrabinda1992
4 ай бұрын
@@asifmolbio and we make heatmap by using those expression values of three biological replicates?
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