Hi ChAMP users:

Can we start the DMR analysis from Beta-matrix, rather than idat, by ChAMP? You know sometimes, we don't have idat, only have beta-matrix (case-control).

Thanks. 

Look at the help page for champ.process().

Looks to me like you should do this:

champ.process(fromIDAT=FALSE, fromFile=TRUE)

and then it will try to read the data in from 'beta.txt' and 'sampleSheet.txt'

> ChAMP:::champ.read
function (betaFile = "beta.txt", sampleSheet = "sampleSheet.txt", 
    resultsDir) 
{
    beta <- read.table(betaFile, header = T, sep = "\t")
    pd <- read.table(sampleSheet, header = T, sep = "\t")
    if (file.exists(resultsDir)) {
        message("The directory ", resultsDir, " already exists. To avoid overwriting please rename in the arguments or delete this folder.")
    }
    else {
        dir.create(resultsDir)
    }
    return(list(beta = beta, pd = pd))
}
<environment: namespace:ChAMP>​

Hello Shicheng:

The latest version of ChAMP support solo beta matrix input, you may try it to solve your problem.I made most function in ChAMP2 support isolated beta matrix and covirate instead of IDAT file.

http://bioconductor.org/packages/release/bioc/html/ChAMP.html

Best

Yuan Tian

Hi,

I have the same problem. I have an excel sheet with all the beta values and probe IDs. I loaded it using read.table but when I run the champ.norm, it does not work and all the subsequent codes fail. Please let me know how to go about it.

Thanks!

Hello:

Could you provide more information about how to exactly do it? I use ChAMP analysis GEO data and TCGA data, all are isolated datasets and works fine. Could you do following things below:

(1): use sessionInfo() to check if you installed latest package (2.2).

(2):paste the error message from champ.norm() here.

Best

Yuan Tian

Now I am wondering if my data in the excel is not in the right format. I have first column with all the probeIDs, followed by Sample Names in the first row and all subsequent rows have the Beta values.

I do have Champ 2.2 and it works fine if I start with IDAT files. I think my problem is with working with the excel/txt file of beta values.

Here is the error message that I get:

[===========================]
[>>>>> ChAMP.NORM START <<<<<<]
-----------------------------
champ.norm Results will be saved in ./CHAMP_Normalization/
[ SWAN method call for BOTH rgSet and mset input, FunctionNormalization call for rgset only , while PBC and BMIQ only needs beta value. Please set parameter correctly. ]

<< Normalizing data with BMIQ Method >>
Note that,BMIQ function may fail for bad quality samples (Samples did not even show beta distribution).
3 cores will be used to do parallel BMIQ computing.
Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(beta)[x],  : 
  task 1 failed - "cannot take a sample larger than the population when 'replace = FALSE'"

Thanks,

Harshika

Hello Harshika:

What dataset are you using? This error often happens when you assign wrong "arraytype" parameter to your dataset. Which means you may inputted EPIC array data, but forget to assign arraytype as "EPIC". So the function would get 450K annotation automatically and do analysis on that. Please check if this is the problem.

Also, I am not very sure if your excel file is correct, but I suggest you to do two things:

(1):Check the format of your matrix, it must be a Matrix or a Dataframe. If so, there should have no problem with Excel file.

(2):Overlap probeID in your file with annotation of 450K or EPIC array, to see if there are some unmatched probes in it, which may cause problem.

Best

Yuan Tian

Thanks Yuan,

However it still not working for me. I also downloaded some GEO data matrix and I am getting the same error:

<< Normalizing data with BMIQ Method >>
Note that,BMIQ function may fail for bad quality samples (Samples did not even show beta distribution).
Error in FUN(X[[i]], ...) : 
  only defined on a data frame with all numeric variables

Not sure whats going on here. Is it somehow assuming the first row i.e. probe IDs also as a part of the data?

Anyways, thank you so much for all the help.

Harshika

Here is the error message that I get:

myNorm <- champ.norm(beta=myLoad$beta,arraytype="450K",cores=5) [===========================]

<h2>[>>>>> ChAMP.NORM START <<<<<<]</h2>

champ.norm Results will be saved in ./CHAMP_Normalization/ [ SWAN method call for BOTH rgSet and mset input, FunctionalNormalization call for rgset only , while PBC and BMIQ only needs beta value. Please set parameter correctly. ]

<< Normalizing data with BMIQ Method >> Note that,BMIQ function may fail for bad quality samples (Samples did not even show beta distribution). 5 cores will be used to do parallel BMIQ computing. Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(beta)[x], : task 1 failed - "could not find function "blc""

Thanks,