User: Chong Kim San Allen

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Posts by Chong Kim San Allen

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Answer: Re: MEDIPS: how does MEDIPS define a methylated region / cluster?
... Dear Lukas, I went back and tried to find those with Inf but I can't. I don't remember where I put the files that contained those values. I did however find those that contained the NA values and I have attached the file containing some of these. I was thinking whether I should use the "transf" pa ...
written 4.9 years ago by Chong Kim San Allen70
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Comment: C: MEDIPS: how does MEDIPS define a methylated region / cluster?
... Dear Lukas, Firstly, thank you so very much for your kind replies. You have been so patient and I am very, very grateful for your help. I have been away and so I'm trying now to gather my thoughts on this again. 1) I did read section 7.7 of the MEDIPS manual. My understanding (correct me if I am w ...
written 4.9 years ago by Chong Kim San Allen70
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Comment: C: MEDIPS: how does MEDIPS define a methylated region / cluster?
... One more thing which I have just come to realize. The rms for some windows are given as 'NA'. What does that mean? Why not just give a value of 0 (zero)? While on the other hand, the rms for some windows are given as 'Inf', which I am assuming is short of "Infinity"? I noticed this tends to be win ...
written 5.0 years ago by Chong Kim San Allen70
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Comment: C: MEDIPS: how does MEDIPS define a methylated region / cluster?
... Dear Lukas, Again, I am so grateful for your quick reply. The only manual for MEDIPS that I know of is this one: http://www.bioc onductor.org/packages/release/bioc/manuals/MEDIPS/man/MEDIPS.pdf and I have looked and just can't find the section 7.7 that you mentioned. The reason I asked about how M ...
written 5.0 years ago by Chong Kim San Allen70
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Comment: C: How does MEDIPS handle multiple mapping of a read
... Dear Lukas Thank you so much for your explanation. I can now understand the problem present by stacked reads. Have a great weekend! Allen ________________________________________ From: Lukas Chavez [lukas.chavez.mailings@googlemail.com] Sent: Thursday, August 28, 2014 6:48 AM To: Chong Kim San All ...
written 5.0 years ago by Chong Kim San Allen70
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Comment: C: How does MEDIPS handle multiple mapping of a read
... Dear Lukas and Wade. Thanks for your replies. It is very much appreciated. Lukas, you mentioned that the internal MEDIPS function getGRange() is set so as to only ignore all unmapped reads and this is done through scanBamFlag. I was wondering if it is possible for me to modify the getGRange() funct ...
written 5.0 years ago by Chong Kim San Allen70
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Downgrading R to an older version
... Hi, My server is running Debian and the most stable version of R for Debian is 2.1.5. I decided to use "apititude install r-base=3.1.0" to install a backport version of R but that command just upgraded it to R 3.1.1. I don't know why it installed 3.1.1 instead of 3.1.0? I have 2 software that I wou ...
medips champ written 5.0 years ago by Chong Kim San Allen70 • updated 5.0 years ago by Dan Tenenbaum8.2k

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