Dude you ahve no idea how helpful you are!! i want to do PhD and before that wanted to learn these bioinformatics and coding skills so that it will help me in future, i did all the normal Python and R classes but never understood the real life use of these in research, today i got some clarity at least. SO THANKSSS Also can you make more such video more such videos and tutorials for food technology perspective it would be grateful.
Nice video! Could you please make one doing the next steps for Microarray analysis? (I mean, filtering data, DE analysis, VolcanoPlot and so on...). Thank you so much. New follower here!
Thank you, great video! Could you please help me with some issues i'm having: I'm trying to execute the annotation (map genes) of a custoum microarray, but with the raw data. That is, I want to make a table with gene names in rows and samples (CEL files) on the columns. Is there a way to execute this procedure of annotation whitout use the normalization functions (like rma or mas5)? Thank you for the attention!
Thank you for this video. How can I perform this kind of analysis on several datasets at once, to boost the number of samples being analyzed? For example, in this video, there were 4 samples in the breast cancer dataset. How would you add more breast cancer datasets to get a larger sample size and a stronger P value? Thank you!
Thank you for this video! May I ask if you were able to account for probes that target similar genes? I noticed in my analysis that there are genes that appeared more than once which could mean that I still need to probably summarize them (i.e., means). Do you perhaps know how to do that?
@bioinformagician thank you so much for these wonderful tutorials. I was wondering if you could please make another video showing downstream analysis of affymetrix data?
This is so wonderful...I enjoyed your video clips...so informative. Just wondering if you have video clips on methylation data analysis and chipseq. Thank you!
Error in getGEOSuppFiles("GSE148537") : Failed to download C:/Users/hp/Documents/GSE148537/GSE148537_RAW.tar! while accessing the GEO dataset, I am getting this error...kindly guide, how to fix this issue?
Thanks a lot for this video. Its really very helpful. Can you please make a video on differential expression analysis of microarray data using limma package? Thank You.. and looking forward to such wonderful videos :)
Thank you for this helpful tutorial! Can you explain why in some cells there are more than one genes separated with "///" and what we should do about them?
@@Bioinformagician Thanks for your reply. I was wondering if you can guide us on how to run DGE analysis on the annotated data like using the LIMMA package. 😊
Hi, I'm using the data from GEO (GSE70947) but my raw.tar file is not in .CEL instead in .txt. How can i read the .txt file using readaffy function? And i wanted to run normalization, how can i do so?
If you click on any one sample and read under 'Data Processing', the values in the text files are already background-corrected and quantile normalized. They should be good to use as is for any downstream analysis.
Thanks a lot for this video . Please can you help with this error am facing with my data at the time of mapping probe id with gene name Using locally cached version of GPL570 found here: C:\Users\RUPESH~1\AppData\Local\Temp\RtmpM3ouSD/GPL570.soft Error in `.rowNamesDF
Hi, I working with some datasets from GEO (GSE686), and I wondering if it's correct to perform RMA normalization and than filter some samples that I want (ex: tumor samples from oral cavity only) or do I need to selected the samples first and performe the normalization? Thank you and congrats for your work, the tutorials are very clear and it's helping me a lot!
As per my understanding, it makes sense to perform RMA normalization on the entire dataset. This will adjust for variations in probe intensities and background noise across samples. Filtering samples before normalization will not account for the technical differences between samples, potentially leading to biased or incorrect results.
hello dear, hope you are doing well. I am practicing this and following you step by step using WINDows operating system. Unfortunately im not able to execute last one that mentions rows_to_columns. Can you please guided me?
normalized.expr % rownames_to_column(var ='ID') %>% inner_join(., feature.data, by = 'ID') Error in normalized.expr %>% rownames_to_column(var = "ID") %>% inner_join(., : could not find function "%>%"
The errors relating to rows_to_columns and "could not find function %>%" is because you are missing a library called 'tidyverse'. Loading the library(tidyverse) first before running the commands will prevent these errors. The steps following differential expression depends on the goal of your analysis. Now that you have differentially expressed genes, what you do want to know about these differentially expressed genes? What biological question you are trying to answer? Typically, differential expression is used when comparing samples from two conditions or when one is trying to identify the effect of treatment on a sample. One could use these differentially expressed genes to get an idea on what pathways are enriched between two conditions or between a treatment group and control group. Analysis like gene ontology enrichment or gene set enrichment analysis are usually performed to get an idea of what GO terms/pathways are enriched.
@@Bioinformagician dear I want to know the genes that are upregulated under abiotic stress in wild v/s domestic plant specie. The microarray data contains wild control, wild stress, domestic control and domestic stress. Can you please guide me in this case? I want to know the set of genes that are more upregulated in wild species than in domestic ones under abiotic stress conditions.
Array (Microarray) values can never be whole numbers because those are probe intensities. You get raw counts data (raw counts = read counts) from RNA-Seq. They are fundamentally different technologies.
Error in getGEOSuppFiles("GSE49072") : Failed to download D:/R- Results/R-Results/GSE49072/GSE49072_RAW.tar! In addition: Warning message: In file.remove(destfile) : cannot remove file 'D:/R- Results/R-Results/GSE49072/GSE49072_RAW.tar', reason 'Permission denied' that is appear when i am doing this commad kindly guide me
Mam , I am not able to download Data . My get GEOSuppFiles is not working. it showing me like that Error in getGEOSuppFiles("GSE93731") : Failed to download C:/Users/DELL/Desktop/R_practice/GSE93731/GSE93731_RAW.tar! In addition: Warning message: In file.remove(destfile) : cannot remove file 'C:/Users/DELL/Desktop/R_practice/GSE93731/GSE93731_RAW.tar', reason 'Permission denied'. Plz Suggest how i can resolve this problem.
Can you try running "chmod -R 755 C:/Users/DELL/Desktop/R_practice/" in the terminal (give write permissions to that folder) and try downloading it again?
@@Bioinformagician I've got a similar error, running R on windows and have given all the permission to read and write files, but still the error persists, any suggestions ? Also some GEO supp files are very huge (2GB or so), can u suggest a workaround to get such data using getGEOsuppfiles
Hi, thank you so much for this video, i dont know why i can't install these packages even if im using the same R version ?? I have to normalize a raw.tar file and i found your interesting video thanks again
M'am The video was really helpful. How can we combine GEO RNA micro array data with RNA seq data? I like to ask you few doubts. Can you share your mail id? Thankyou
You cannot combine data which have different gene quantifications units like microarray and RNA-Seq. You can find my email ID in the description section of every video.
Hey, I am getting an error while downloading the supplementary file, it shows - Error in getGEOSuppFiles("GSE107462") : Failed to download /Users/hp/Desktop/R_DGE/GSE107462/GSE107462_RAW.tar! can you please help me with this
Oh my god! I was breaking my head on the internet to extract these tar files. You made it so simple. Thank you life-saver !!
I LOVE YOU!!!! I've been struggling with this for a few days and your video is such a lifesaver!
This is so useful, literally saving whole days of googling and trial and errors. Thank you so much!
Dude you ahve no idea how helpful you are!! i want to do PhD and before that wanted to learn these bioinformatics and coding skills so that it will help me in future, i did all the normal Python and R classes but never understood the real life use of these in research, today i got some clarity at least. SO THANKSSS Also can you make more such video more such videos and tutorials for food technology perspective it would be grateful.
This is great helpful. Please upload more videos about .CEL files normalization and integration for many datasets
can u plz make a demo tutorial on using Limma for differential expression of microarray data
Nice video! Could you please make one doing the next steps for Microarray analysis? (I mean, filtering data, DE analysis, VolcanoPlot and so on...). Thank you so much. New follower here!
Thank you for the suggestion. I shall surely plan on making a video on it soon :)
Thank you, great video!
Could you please help me with some issues i'm having: I'm trying to execute the annotation (map genes) of a custoum microarray, but with the raw data. That is, I want to make a table with gene names in rows and samples (CEL files) on the columns. Is there a way to execute this procedure of annotation whitout use the normalization functions (like rma or mas5)? Thank you for the attention!
Thank you for this video. How can I perform this kind of analysis on several datasets at once, to boost the number of samples being analyzed? For example, in this video, there were 4 samples in the breast cancer dataset. How would you add more breast cancer datasets to get a larger sample size and a stronger P value? Thank you!
it was so clear and you are amazing) thank you!
can we run multiple geo datasets for this r script or do it individually.(all datasets are of affymetrix)
Thank you for this video! May I ask if you were able to account for probes that target similar genes? I noticed in my analysis that there are genes that appeared more than once which could mean that I still need to probably summarize them (i.e., means). Do you perhaps know how to do that?
Usually I group by genes and take a rowSum and keep the row with max rowSum.
@@Bioinformagician how do you exactly do this? I'm sorry. I'm kinda new to R
@bioinformagician thank you so much for these wonderful tutorials. I was wondering if you could please make another video showing downstream analysis of affymetrix data?
This is so wonderful...I enjoyed your video clips...so informative. Just wondering if you have video clips on methylation data analysis and chipseq. Thank you!
I am glad you find my videos informative. Yes, I shall be making videos covering epigenetic data analysis in the future :)
how to make models for LIMMA analysis from above normalized data ?
Error in getGEOSuppFiles("GSE148537") : Failed to download C:/Users/hp/Documents/GSE148537/GSE148537_RAW.tar!
while accessing the GEO dataset, I am getting this error...kindly guide, how to fix this issue?
For others if they get same issue:
library(curl)
options(timeout = max(300, getOption("timeout")))
options(download.file.method.GEOquery = "curl")
It's really helpful, thank you so much
Hey that inner join last steps is not working can u suggest
Thanks a lot for this video. Its really very helpful. Can you please make a video on differential expression analysis of microarray data using limma package? Thank You.. and looking forward to such wonderful videos :)
Thank you for the suggestion, I will surely plan on making a video on it :)
Thank you for this helpful tutorial! Can you explain why in some cells there are more than one genes separated with "///" and what we should do about them?
Is there any way to sort the samples in the x axis into "cancer" and "normal tissue"? Thanks !
How to retrieve these Normalized.expr file from environment?
please can you answer me, what about if data was txt format, i mean 10 file of GSM......txt how i can open it
Really helpful video!. Thanks. I'm trying to do gene expression analysis and I'm new to R, What do i do next. Please help.
can you show me how to fix this error feature.data
Thanks for the video :) Helped a lot!
Excellent video. Could you please make a video on the downstream processes in DGE analysis after annotating the microarray data?
You mean gene set enrichment analysis or pathway analysis using differentially expressed genes?
@@Bioinformagician Thanks for your reply. I was wondering if you can guide us on how to run DGE analysis on the annotated data like using the LIMMA package. 😊
I will surely plan on making a video covering that. Thanks for the suggestion :)
@@Bioinformagician is DGE analysis of micro array data is available?
@@Bioinformagician please use the same data set for differential gene expression. Thanks
Thanks a lot, @Bioinformagician. Could you please show us how to use Limma for the differential expression of microarray data?
Hi, I'm using the data from GEO (GSE70947) but my raw.tar file is not in .CEL instead in .txt. How can i read the .txt file using readaffy function? And i wanted to run normalization, how can i do so?
If you click on any one sample and read under 'Data Processing', the values in the text files are already background-corrected and quantile normalized. They should be good to use as is for any downstream analysis.
It is amazing way for teaching! thausend thanks!
Nice video! I got some *.txt file but not .cel files, what should I do to normalize these data?
Thanks a lot for this video . Please can you help with this error am facing with my data at the time of mapping probe id with gene name
Using locally cached version of GPL570 found here:
C:\Users\RUPESH~1\AppData\Local\Temp\RtmpM3ouSD/GPL570.soft
Error in `.rowNamesDF
ma'am, is this all possible in Python?
Hi, I working with some datasets from GEO (GSE686), and I wondering if it's correct to perform RMA normalization and than filter some samples that I want (ex: tumor samples from oral cavity only) or do I need to selected the samples first and performe the normalization? Thank you and congrats for your work, the tutorials are very clear and it's helping me a lot!
As per my understanding, it makes sense to perform RMA normalization on the entire dataset. This will adjust for variations in probe intensities and background noise across samples. Filtering samples before normalization will not account for the technical differences between samples, potentially leading to biased or incorrect results.
hello dear, hope you are doing well. I am practicing this and following you step by step using WINDows operating system. Unfortunately im not able to execute last one that mentions rows_to_columns. Can you please guided me?
and also what are the next steps differential expression. Kindly share the next steps aswell. Im a PhD. Scholar and I really want guidance.
normalized.expr %
rownames_to_column(var ='ID') %>%
inner_join(., feature.data, by = 'ID')
Error in normalized.expr %>% rownames_to_column(var = "ID") %>% inner_join(., :
could not find function "%>%"
The errors relating to rows_to_columns and "could not find function %>%" is because you are missing a library called 'tidyverse'. Loading the library(tidyverse) first before running the commands will prevent these errors.
The steps following differential expression depends on the goal of your analysis. Now that you have differentially expressed genes, what you do want to know about these differentially expressed genes? What biological question you are trying to answer?
Typically, differential expression is used when comparing samples from two conditions or when one is trying to identify the effect of treatment on a sample. One could use these differentially expressed genes to get an idea on what pathways are enriched between two conditions or between a treatment group and control group. Analysis like gene ontology enrichment or gene set enrichment analysis are usually performed to get an idea of what GO terms/pathways are enriched.
@@Bioinformagician dear I want to know the genes that are upregulated under abiotic stress in wild v/s domestic plant specie. The microarray data contains wild control, wild stress, domestic control and domestic stress. Can you please guide me in this case? I want to know the set of genes that are more upregulated in wild species than in domestic ones under abiotic stress conditions.
@@KhanapeenaorGupShup You need to perform a differential gene expression analysis to find genes upregulated in one group compared to another.
thanks mam it is very effective
I want to get the raw count data from profiling by array is it possible (whole numbers) ?
Array (Microarray) values can never be whole numbers because those are probe intensities. You get raw counts data (raw counts = read counts) from RNA-Seq. They are fundamentally different technologies.
So can we perform loess normalization on raw counts (from RNA-Seq)? Because I was trying but raw count was not normalized @@Bioinformagician
you are the best!
What can you use if affy package no longer exist for microarray expression data?
You could try oligo package provided your array is Affymetrix or NimbleGen
where to find affy package and how to install it? thanks
bioconductor.org/packages/release/bioc/html/affy.html
Thank You this helped me lot !!!,
I have some files with TXT how to read and normalize data for txt files. example GSE74685
Thanks very much, It is very informative video. Is it possible to continue it with analysis of this data and visualization it with heat mapping?
Excellent video, but how can I normalise Agilent data with .txt.gz file format.
Check out this thread: www.biostars.org/p/388949/
Thank you very much.
Error in getGEOSuppFiles("GSE49072") :
Failed to download D:/R- Results/R-Results/GSE49072/GSE49072_RAW.tar!
In addition: Warning message:
In file.remove(destfile) :
cannot remove file 'D:/R- Results/R-Results/GSE49072/GSE49072_RAW.tar', reason 'Permission denied'
that is appear when i am doing this commad kindly guide me
Mam there is different file instead of cel of which I am working on ....the data is not generating help me plz...
Can you confirm it is an Affymetrix array that you are looking at?
@@Bioinformagician it's agilent
@@yashangchekar402 Check out this thread: www.biostars.org/p/388949/
Mam , I am not able to download Data . My get GEOSuppFiles is not working. it showing me like that
Error in getGEOSuppFiles("GSE93731") :
Failed to download C:/Users/DELL/Desktop/R_practice/GSE93731/GSE93731_RAW.tar!
In addition: Warning message:
In file.remove(destfile) :
cannot remove file 'C:/Users/DELL/Desktop/R_practice/GSE93731/GSE93731_RAW.tar', reason 'Permission denied'. Plz Suggest how i can resolve this problem.
Can you try running "chmod -R 755 C:/Users/DELL/Desktop/R_practice/" in the terminal (give write permissions to that folder) and try downloading it again?
@@Bioinformagician I've got a similar error, running R on windows and have given all the permission to read and write files, but still the error persists, any suggestions ? Also some GEO supp files are very huge (2GB or so), can u suggest a workaround to get such data using getGEOsuppfiles
Thank you for this video !!
I have a question di .. kindly help me
thanks you !!
Hi, thank you so much for this video, i dont know why i can't install these packages even if im using the same R version ?? I have to normalize a raw.tar file and i found your interesting video thanks again
What system are you using? Do you see any specific error?
Bravo
M'am The video was really helpful. How can we combine GEO RNA micro array data with RNA seq data? I like to ask you few doubts. Can you share your mail id? Thankyou
You cannot combine data which have different gene quantifications units like microarray and RNA-Seq. You can find my email ID in the description section of every video.
Hey, I am getting an error while downloading the supplementary file, it shows - Error in getGEOSuppFiles("GSE107462") :
Failed to download /Users/hp/Desktop/R_DGE/GSE107462/GSE107462_RAW.tar! can you please help me with this