How to calculate log2fold change / p value / how to use t test in excel

In this video we will try to calculate the p value through t test in excel to know wither expression data of our gene is significantly changed or not in response to specific treatment. Then we will calculate the log2fold change to check that this change in expression is positive and negative, and how much. This all work, we will do in excel.
#log2_vlaue
#fold_change
#t_tets
#p_value

[@maryamsediqi3726]

Word of thanks is not enough for your such nice, easy and useful explanation.

[@genomewidestudy]

Thanks for your comment.
Acknowledged

[@davidguardamino]

Thank you for your video, it has been very demostrative. I would recommend to add and adjusted p-value column to deal with the false discovery rate. thank you so much

[@genomewidestudy]

Thanks for your suggestion.
appreciated sir

[@castilloh.gianmarco1048]

Great, thanks for the video, although I can't translate it into Spanish but I have been able to understand it with the little English I speak, thanks, good luck with everything.

[@genomewidestudy]

Glad to hear that! It's your hardwork

[@Abdullah-ex6vd]

Thanks. Very impressive keep it up.

[@genomewidestudy]

Thanks a lot!

[@amrsalaheldinabdallahhammo663]

You are genius !!! Thanks a lot

[@genomewidestudy]

Thanks for comment.

[@Nature520-k6i]

Very informative. Your videos are helping me a lot in. my analysis

[@genomewidestudy]

Great to hear! Thanks for comment

[@nikitrianta9896]

Easy to understand thank you!

[@genomewidestudy]

Glad it helped!

[@Nature520-k6i]

MashaAllah. very informative video

[@genomewidestudy]

Many many thanks

[@billywang1409]

thank you so much, this vedio help me a lot

[@genomewidestudy]

Thanks for your comment

[@gulsum9771]

GRAZIE MILLEEE

[@genomewidestudy]

............?

[@fahmidazamanirin]

oh no, you saved my time during my thesis work. Could you please make a video for good bar plot for fold change of gene expression? I already calculated my Cq data by using delta delta Cq method for fold change. I did not follow your method. Now little bit confused about my data. Do I follow your way by using my qPCR data?

[@genomewidestudy]

yes, you can

[@hafizmuhammadahmad5314]

Sir, Guide how to analyse gene expression from RNA seq data
?

[@mahakhan4468]

Excellent Dr sahib

[@genomewidestudy]

Thanks for watching. Appreciated

[@wasifkulachi8723]

Very impressive.

[@genomewidestudy]

Thanks for watching. Appreciated

[@waqarali4721]

Really helpful. Please also make video that how we can calculate the P and logFC value of a dataset from GEO

[@genomewidestudy]

you can use the same procedure with data from GEO...

[@waqarali4721]

@@genomewidestudy The GEO dataset analyzed by high throughput sequencing don't have three three replicated in that case how we can calculate the P-Value and LogFc value ? Thanks in advance for your sincere cooperation

[@genomewidestudy]

for logFC, it need only means. which is available in GEO dataset

[@castilloh.gianmarco1048]

@@genomewidestudy Could you be kind to explain us, in a new video for the channel?
p-value and logFC.
salute.

[@lroseteable]

@@genomewidestudy can medians be used for log2FC? Or is it always the mean? Thank you in advance.

[@polycarpnalela6951]

Thanks very much. Very informative

[@genomewidestudy]

Glad it was helpful!

[@polycarpnalela2315]

This was very helpful. Thank you

[@genomewidestudy]

Glad it was helpful!

[@sunnyyoda5511]

VERY GOOD!!!!

[@genomewidestudy]

Thanks for watching

[@Gbemi78]

thanks for these upload. Helpful as always

[@genomewidestudy]

thanks for comment,
please watch like and share,
so get some encourage

[@jasvinderkaur4697]

Thank you sir for a wonderful video,I have a doubt regarding normalisation, you have not normalised your data with the CT value of housekeeping gene? Is p value calculated after normalisation or before

[@genomewidestudy]

its expression data after normalization or you can say calculation.

[@genomewidestudy]

The normalization method is described in the following video
qRT-PCR Part 01 How to do qRT-PCR step by step from cDNA to PCR
qRT-PCR Part 02 How to analyse qRT-PCR data for gene expresion ∆∆ct Method for Real Time PCR data

[@goodtimewithhajira]

GOOD

[@genomewidestudy]

Thanks for watching. Appreciated

[@jalilahmad9923]

JazaKALLAH Sir

[@depthinnature]

Great job brother.

[@genomewidestudy]

Thank you! Cheers!

[@MogosCatalin]

Thank you!!

[@genomewidestudy]

Thanks for watching. Appreciated

[@KN-tx7sd]

sorry, one more thing, can you please explain how to add a column on multiple corrections using either the Benjamini Hochberg method or the Bonferroni method. Thank you

[@genomewidestudy]

Sorry I cant understand your question

[@kelseywilson278]

I am a little bit confused on the values used. Are these Ct values? If not, can Ct values be used? Do they have to be normalized to the reference gene first?

[@genomewidestudy]

These are the expression data of the genes.
We get the Ct values from qPCR and calculate the expression data from that Ct values.
After calculating Ct vlues then we use these methods to get the log2fold change or significnt of our data..
You can also check the video in which I have described that how to calculate expression data from Ct values..

[@genomewidestudy]

qRT PCR Part 01
qRT PCR Part 02 How to analyze qRT PCR data for gene expresion | ∆∆ct Method for Real-Time PCR data

[@georgyjogen2859]

Nice video, but i think in fold change explanation @1:57 "(when B > A)" and "(A > B)" is wrong right? or am i missing something. It should be vice versa right.

[@genomewidestudy]

Thanks for your valuable comment. I will check

[@Muhammad_Hafeez]

Very nice

[@genomewidestudy]

Thanks for watching. Appreciated

[@bonhommemaelle1322]

Hello, thank you for the informative video,
I would like to calculate log2 Fold Change of my data.
My datas have already been log10 transformed for other analysis. How should I calculate log2 Fold Change on log10 data? Thank you in advance

[@genomewidestudy]

Video is uploaded about log10 to log2 data. Please have a look. Thanks

[@amanidhiflaoui5322]

Thank you so much for this video! Just a question about the triplicates, how did you calculate these values ? For example for CK R1: Ct CK R1 target - Ct CK R1 reference gene ?

[@genomewidestudy]

All three are Ck?

[@genomewidestudy]

Please clarify your Question.

[@amanidhiflaoui5322]

I am asking how you calculated the value of each ck. For example CK R1 gene 1: we have 4.03. how you get this value ? Did you use the ct target - ct reference?

[@amanidhiflaoui5322]

Also regarding the Log2 Fc, I obtained a negative values in mean so when apply the rule to calculate Log2 it couldn't calculated because i have a negative value! Can please explain this?

[@genomewidestudy]

These are the expression values and calculated from Ct values.

[@shiyuren]

Thank you for your video very much! I have a question: Is it necessary to perform the normality test and the Levene test before we choose T test or Mann-Whitney test?

[@genomewidestudy]

i think literature will give you better answer. After considering the literature, Still have confusion then let me know. Thanks,

[@elMARABIYOCHO1989]

Thank you for your video. I have a question. I have two cultures (control and infected). I measure the protein abundance of different proteins for both samples at timepoint = and time point 25 minutes. What would be the best way to go about analyzing my data? Do I calculate the fold change of control from T0 and T25 and then compare it with the fold change of the infected from T0 and T25?

[@genomewidestudy]

You mean you have two samples control and treated, and you have taken the data of both samples at two times span.
1. Taken the data of both samples (control and treated) at 0 minutes
2. taken the data of both samples (control and treated) at 25 minutes.
Am I right?

[@elMARABIYOCHO1989]

@@genomewidestudy yes.

[@genomewidestudy]

1. you can calculate the fold change of control and treated at 0 min
2. also calculate the fold change at 25 min.
then discuss the comparison that your gene's activity how much increase or decrease at 0 and 25 min

[@elMARABIYOCHO1989]

@@genomewidestudy Also wanted to ask how I would go about calculating the p-value of this.

[@elMARABIYOCHO1989]

@@genomewidestudy Okay. Thank you so much for your reply. I would also like to do a volcano plot of log2fold change against -log10 p value. Do I then need two separate graphs for each time point?

[@dr.mohdaamir6688]

Sir, you have calculated significant genes based on p-value Why?. It would be more appropriate if it would have been calculated based on Adjusted p-value.

[@genomewidestudy]

yes, you are right. Thanks for suggestion. appreciation from the heart.

[@saraswatishelke643]

1) Values taken for control and treatment are fold change values? Calculated using 2 raise to minus delta delta Ct?
2) what if I have to calculate for multiple treatments and genes?

[@genomewidestudy]

If you use multiple treatment or genes then you will use Factorial ANOVA

[@saraswatishelke643]

@@genomewidestudy are those values mentioned fold change values calculated using 2 raised to minus delta delta Ct then taking log of ratio?

[@genomewidestudy]

Which values.
If you are talking about the values in the video I used qs examples then these CT values that we get from qRT PCR

[@saraswatishelke643]

@@genomewidestudy Thank you

[@muhammadmubeen8192]

if we have 4 replications of control and 3 replications of then how to calculate p value in excel?

[@genomewidestudy]

doesn't matter, you can use, when you select array1, you can select all 4 replications

[@KN-tx7sd]

can the same be done in R, many thanks

[@genomewidestudy]

Sorry, I don't know much about R. May be you can.

[@nakachewminuye5291]

how can we calculate p-value for control vs treated without replicates?

[@genomewidestudy]

I think experiment is incomplete without replications...

[@genomewidestudy]

If you have mean data, then I will try to make video on it ..

[@muthukumarb1326]

@@genomewidestudy But cuffdiff, edgeR are still give p values even there is no without technical replicates... Do you have any idea how they are calculating without replicates? If you know please post here

[@siya1999]

How can we calculate p adjusted value?

[@genomewidestudy]

Already made the video on topic. you will simply find it with the title
calculate Log2fold change, p adj, significant, non significant expression Genome wide study
or
convert p value into p adj value #Genome wide study #statisticalanalysis

[@praveenjohn7594]

HOW WE CAN CALCULATE ADJ P VALUE TO FOLD CHANGE VALUE

[@genomewidestudy]

Already made the video on topic
calculate Log2fold change, p adj, significant, non significant expression
or
convert p value into p adj value #Genome #statisticalanalysis