User: hseepany

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hseepany0
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Posts by hseepany

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Comment: C: ChAMP input: Beta Matrix?
... So after I made sure that the probe ID is  rowname, and sample name is in the colname, now I get the following error. << 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 d ...
written 2.8 years ago by hseepany0
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Answer: A: ChAMP input: Beta Matrix?
... 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 ...
written 2.8 years ago by hseepany0
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Answer: A: ChAMP input: Beta Matrix?
... 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 work ...
written 2.8 years ago by hseepany0
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Answer: A: ChAMP input: Beta Matrix?
... 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! ...
written 2.8 years ago by hseepany0
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New to R: How to use your own data for Bioconductor Packages
... Hi, I am new to R and programming and I have a couple of BAM files that I wanted to use to look at methylation patterns using MEDIPS. I was wondering how can I use my BAM files to compare the data. When I add my file location to the commands, it does not work. Please help. It will also be very help ...
rsamtools medips written 4.0 years ago by hseepany0 • updated 4.0 years ago by Dan Tenenbaum8.2k

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