User: pm2015
pm2015 • 0
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Posts by pm2015
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... Hello
I am interested in using Baymeth available form Repitools package to calculate absolute methylation levels for my MBD-seq data. However, I do not have a matched ssl control. I saw the paper mention analysis without including the ssl control. However, I wasn't able to figure out how to do this ...
written 3.3 years ago by
pm2015 • 0
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... Thank you for replying.
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written 3.7 years ago by
pm2015 • 0
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... Thanks again. I appreciate you taking time to answer my questions.
So for my dataset, would fold change be the only criteria to filter the genes to further interrogate? In the past, when analyzing similar datasets with other tools, I used a combination of fold change and p-values. Is there a way to ...
written 3.7 years ago by
pm2015 • 0
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... Thanks for your reply. I do understand that this is not the best dataset as it is without replicates. Cost issues prohibited the lab to include replicates and it seems the experiment was designed by someone not very familiar with statistical analyses for microarrays. I am trying my best to get some ...
written 3.7 years ago by
pm2015 • 0
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... Thanks for pointing it out. Sorry for the confusion. I have edited my post.
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written 3.7 years ago by
pm2015 • 0
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... Hi
I am trying to analyse an agilent two-color dataset with a direct experimental design (no reference). It consists of paired (treated and untreated samples) for each time point hybridized to a single array. The data is in two cell lines (denoted as M & P). I am trying to construct a design ma ...
written 3.7 years ago by
pm2015 • 0
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... Hello All
I am trying to process my Illumina 450 K methylation array data using Minfi but I keep getting the following error after using the function dmpFinder.
Error in smooth.spline(lambda, vec.p0, w = ncs.weights, df = 3) :
missing or infinite values in inputs are not allowed
In addition: W ...
written 3.8 years ago by
pm2015 • 0
• updated
3.8 years ago by
Kasper Daniel Hansen ♦ 6.4k
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... Hello All
I am trying to process my Illumina 450 K methylation array data using Minfi but I keep getting the following error after using the function dmpFinder.
Error in smooth.spline(lambda, vec.p0, w = ncs.weights, df = 3) :
missing or infinite values in inputs are not allowed
In addition: W ...
written 3.8 years ago by
pm2015 • 0
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... Thanks a lot. I will proceed as you suggested.
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written 4.0 years ago by
pm2015 • 0
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... Hi Gordon
Thanks for your reply. From the name of the files it does seem like RNA from the same condition has been hybridized to both channels. I do not have any further info on the hybridizations besides the names of the files themselves. I really don't understand why they were done this way.
Sor ...
written 4.0 years ago by
pm2015 • 0
• updated
4.0 years ago by
Gordon Smyth ♦ 38k
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