single excel file containing methylation beta values does not get loaded in ChAMP
0
0
Entering edit mode
@7e6bfb3b
Last seen 17 days ago
Bangladesh

Hello, I have an excel sheet with all the beta values and probe IDs. I also created a pd file in the same directory (containing sentrix id, sentrix position etc). However when I try to load these files in ChAMP using either champ.import or champ.load function I get the error that pd file does not match with green channel idat file. I am very confused about how to load this excel sheet into champ. I don't even have idat files. Can anyone help me?

[===========================]

[<<<< ChAMP.IMPORT START >>>>>]

[ Section 1: Read PD Files Start ]

CSV Directory: E:/new project ideas/march, 2024/data/figures/methylation/analysis/pd.csv

Find CSV Success

Reading CSV File

Replace Sentrix_Position into Array

Replace Sentrix_ID into Slide

Error in champ.import("E:/new project ideas/march, 2024/data/figures/methylation/analysis") :

Error Match between pd file and Green Channel IDAT file.

Thanks a lot! Tahirah

```

ChAMP • 142 views
ADD COMMENT
0
Entering edit mode

"champ.load() can not perform filtering on beta matrix alone. For users have no .IDAT data but beta matrix and Sample_Sheet.csv, you may want perform filtering using the champ.filter() function and then use following functions to do analysis."

If you have no .idat files but a beta matrix, you should start at the champ.filter() step

ADD REPLY

Login before adding your answer.

Traffic: 971 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6