User: pm2015

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pm20150
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Posts by pm2015

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Analysis of MBD-seq data without ssl control using BayMeth
... 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 ...
repitools methylation baymeth mbd-seq written 2.9 years ago by pm20150
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Comment: C: Limma Design Matrix for two channel agilent arrays (direct experimental design)
... Thank you for replying.  ...
written 3.3 years ago by pm20150
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Answer: A: Limma Design Matrix for two channel agilent arrays (direct experimental design)
... 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 3.3 years ago by pm20150
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Comment: C: Limma Design Matrix for two channel agilent arrays (direct experimental design)
... 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 3.3 years ago by pm20150
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Comment: C: Limma Design Matrix for two channel agilent arrays (direct experimental design)
... Thanks for pointing it out. Sorry for the confusion. I have edited my post.  ...
written 3.3 years ago by pm20150
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Limma Design Matrix for two channel agilent arrays (direct experimental design)
... 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 ...
twochannel limma agilent limma design matrix written 3.3 years ago by pm20150
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Error processing Infinium 450K Methylation data using Minfi
... 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 ...
minfi methylation software error illumina450k written 3.4 years ago by pm20150 • updated 3.4 years ago by Kasper Daniel Hansen6.4k
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Error processing Infinium 450K Methylation data using Minfi
... 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 ...
minfi methylation software error illumina450k written 3.4 years ago by pm20150
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Comment: C: Single channel analysis of two-color agilent array using limma
... Thanks a lot. I will proceed as you suggested. ...
written 3.6 years ago by pm20150
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Comment: C: Single channel analysis of two-color agilent array using limma
... 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 3.6 years ago by pm20150 • updated 3.6 years ago by Gordon Smyth37k

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