How to read and normalize microarray data in R - RMA normalization | Bioinformatics 101

Thank you very much.

Mam, am not able to download Data. My get GEOSuppFiles is not working. it showing me like that
Error in getGEOSuppFiles ("GSE48350") :
Failed to download C:/Users/vaishnavi mohite/Downloads/GSE48350/GSE48350_RAW.tar!
In addition: Warning message:
In file.remove (destfile) :
cannot remove file 'C:/Users/vaishnavi mohite/Download/GSE48350/GSE48350_RAW.tar',
reason 'Permission denied'. Plz Suggest how i can resolve this problem.

@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?

How to retrieve these Normalized.expr file from environment?

I want to get the raw count data from profiling by array is it possible (whole numbers) ?

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!

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

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.

Is there any way to sort the samples in the x axis into "cancer" and "normal tissue"? Thanks !

where to find affy package and how to install it? thanks

Thank you mam very helpful this video for me. i have one doubt mam when we give gse in getGEOSuppFiles("GSE148537") more than one gse it accepts mam or we use any other function for that .. mam ..

I have a question di .. kindly help me

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?

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

Nice video! I got some *.txt file but not .cel files, what should I do to normalize these data?

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 !!

What can you use if affy package no longer exist for microarray expression data?

Excellent video, but how can I normalise Agilent data with .txt.gz file format.

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<-`(x, value = value) : invalid 'row.names' length

Mam there is different file instead of cel of which I am working on ....the data is not generating help me plz...

please can you answer me, what about if data was txt format, i mean 10 file of GSM......txt how i can open it

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?

you are the best!

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.

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?

Thank you for this video !!

Thanks a lot for this video,Please can i contact to you by email or whatsapp?

Bravo

Thanks for the video :) Helped a lot!

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?

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. Could you please make a video on the downstream processes in DGE analysis after annotating the microarray data?

It is amazing way for teaching! thausend thanks!

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?

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 <3

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!

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 :)

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

it was so clear and you are amazing) thank you! <3

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!

thanks you !!

It's really helpful, thank you so much