Genome wide Methylation Analysis using R - Champ Tutorial

#Bioconductor #Differential #Methylation #Analysis #Genome #Bigdata #Datascience #DMR #DMP #Dataanalysis #Rstudio #Packages
CHAMP is an R package to analyze whole genomic methylation data. The step wise tutorial will guide you through the commands needed for differential methylation analysis using whole genome chip data.
Following is the link for other details:
www.bioconduct...
Blog: farhanhaqjahan......
RUclips: / farhanhaqj​

[@farhanazhwinmaulana-1298]

What a very insightful and understandable tutorial for beginners working on genome-wide epigenetic analysis. Do you have other practical videos describing the process of extracting these methylation dataset (according to the staging levels of cancer) from publicly available resources ?. Thank you

[@medeeabadii2702]

Thank you for this great tutorial! One question though on an important aspect, how did you generate the input file? Or did you just create it manually?

[@FarhanHaqj]

Manually in this video.

[@sabanasir7223]

Could you do a overlap/mapping of our methylation analysis differently methylated gene with database gene sets using LOLA from rnbeads in depth please

[@szanar8422]

Thank you it helped a lot!!! I would've spent like days figuring everything out if it wasn't for your tutorial😶

[@FarhanHaqj]

Pleasure

[@pramod_pal]

Very nice tutorial. Thanks a lot

[@ThiagoBenazziMaia]

Really, really helpfull

[@luiscano2193]

good tutorial... why you don't use Rsutdio ?

[@FarhanHaqj]

Thank you for suggestion. In next videos I used Rstudio

[@felipemunozgonzalez8188]

Great tutorial, very clear. Also can teach us Bismark or something related to whole genomic methylation? thanks

[@FarhanHaqj]

Thanks. Will check and see what i can do for you!

[@Adelphos0101]

This looks like a very nice tutorial. I'm trying to analyze a dataset from GEO (GSE129841) and it doesn't provide idat files but a txt with the methylated and unmethylated probe intensity signals in columns for each sample. Can ChAMP analyze data in these format or is it possible to create idat files from it?
I hope you can help me.

[@hiago1159]

I have the same problem. Did you manage to find a solution?

[@CameronSugden-jj1yr]

how would one go about using multiple phenotypes in the champ.DMP process?

[@pramod_pal]

Please make next video on RNAseq analysis, differential gene expression analysis using R.
I am waiting for the next video. 🤘

[@FarhanHaqj]

Two videos including Deseq and EdgeR are already uploaded. Thanks

[@pramod_pal]

@@FarhanHaqj thank you

[@explorewithdrk2295]

I have TCGA level3 methylation files not IDAT files. Can i use this ? I need help with input files.

[@user-ku2po2by4k]

How can I get Sample Sheets.csv if it was not available in the repository?

[@user-tv1wr8qd4n]

very informative brother one thing please how i can inbox you

[@MrArun1421]

Hi Farhan, Very good tutorial. I exactly prepared the 'sample input' file as you described in your tutorial. But I got a warning and finally an error message. Warning:
"Find CSV Success
Reading CSV File
Replace Sentrix_Position into Array
Replace Sentrix_ID into Slide
There is NO Sample_Well in your pd file.
[ Section 1: Read PD file Done ]". Error:
Failed CpG Fraction.
1A NaN
2A NaN
3A NaN
4A NaN
5A NaN
6A NaN
7A NaN
1B NaN
2B NaN
3B NaN
4B NaN
5B NaN
6B NaN
7B NaN
8A NaN
9A NaN
10A NaN
11A NaN
8B NaN
9B NaN
10B NaN
11B NaN
Error in if (any(numfail >= SampleCutoff)) { :
missing value where TRUE/FALSE needed
In addition: There were 45 warnings (use warnings() to see them)

[@puspitasaha3412]

As I am entering the champ.load command, the following error message is displayed "[===========================]
[>>]
-----------------------------
[ Loading Data with ChAMP Method ]
----------------------------------
Note that ChAMP method will NOT return rgSet or mset, they object defined by minfi. Which means, if you use ChAMP method to load data, you can not use SWAN or FunctionNormliazation method in champ.norm() (you can use BMIQ or PBC still). But All other function should not be influenced.
[===========================]
[>>]
-----------------------------
[ Section 1: Read PD Files Start ]
CSV Directory: D://ChAMPdata/inst/extdata/lung_test_set.csv.csv
Find CSV Success
Reading CSV File
Replace Sentrix_Position into Array
Replace Sentrix_ID into Slide
[ Section 1: Read PD file Done ]
[ Section 2: Read IDAT files Start ]
Loading:D://ChAMPdata/inst/extdata/7990895118_R03C02_Grn.idat ---- (1/8)
Error in FUN(X[[i]], ...) : could not find function "readIDAT"
Please tell what I should do to solve the could not find function "readIDAT" error?

[@lm7666]

This is bad