User: stb

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stb0
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Posts by stb

<prev • 8 results • page 1 of 1 • next >
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Answer: A: MeDIPS: warning when using "ttest" settings in MEDIPS.meth
... Dear Lukas,  We have made a new observation concerning the 'ttest' functionality.  If I have two groups with 5 and 6 replicates, and then compare the run of MEDIPS.meth with diff.method set to 'ttest' or 'edgeR', with diffnorm set to 'rpkm' and 'tmm', respectively, there is a huge difference in th ...
written 5 months ago by stb0
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How does the function MEDIPS.CpGenrich work?
... Hi,  I have a question regarding the MEDIPS.CpGenrich function. I have done a MeDIP-seq experiment. I go many more reads back from sequencing than expected. As an example, after filtering in Galaxy a total of 58,712,585 first mate reads are imported to MEDIPS for one of the samples.  With this de ...
medips written 6 months ago by stb0 • updated 6 months ago by Lukas Chavez470
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Insertion size when using 'paired' in MEDIPS.createSet()
... Hi,  I have a question concerning insertion size when using MEDIPS. When setting paired = TRUE in MEDIPS, you will get a mean insertion size as well as standard deviation; Mean insertion size: 204.4319 nt SD of the insertion size: 57.93392 nt Max insertion size: 602 nt Min insertion size: 49 nt ...
medips R medip-seq pair-end reads written 11 months ago by stb0 • updated 11 months ago by Lukas Chavez470
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How does the 'paired' argument works in MeDIPS 1.23.2
... Hi, I have some question regarding the ‘paired’ argument and how to use it in MeDIPS (version 1.23.2) If ‘paired’ = true, are the arguments ‘extend’ and ‘shift’ then ignored automatically? If ‘paired’ = true, how does normalization with rpkm then works? Is it only based on the reads (as the nam ...
medips R medip-seq pair-end reads written 14 months ago by stb0 • updated 14 months ago by Lukas Chavez470
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Comment: C: MeDIPS: warning when using "ttest" settings in MEDIPS.meth
... Dear Lukas,  I checked the p.values and adjusted p values. As expected the p.values are identical within a window, and the adjusted p values are different using the ttest with different minRowSum.   It makes sense with the different numbers of windows then. Maybe I can increase the minRowSum when ...
written 15 months ago by stb0
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Comment: C: MeDIPS: warning when using "ttest" settings in MEDIPS.meth
... Dear Lukas, Thanks for your reply. I’ve looked in to it in more details in order to provid the needed information. The warning comes up after the “Adding differential coverage results…”, and I do get a result table, as I describe in detail here: If I run the following command: TEST1 MEDIPS.met ...
written 15 months ago by stb0
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MeDIPS: warning when using "ttest" settings in MEDIPS.meth
... Hi,  I'm currently working with my MeDIP-seq data using MEDIPS in R. I have 18 IP samples (no Input) in 3 groups with PE50. For mapping, I have used bwa for Illumina with default settings in Galaxy. Arguments for creating MEDIPS SET:  BSgenome <- 'BSgenome.Mmusculus.UCSC.mm9' uniq <- 1e-3 ...
medips R medip-seq written 15 months ago by stb0
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MeDIPS and use of the 'bwa' parameter
... Hi,  I've done MeDIP-seq (paired-end, 50 bp reads) with 18 samples from three groups and  I would like to compare them using MeDIPS.  For mapping, I used bwa.  From other questions in here, https://support.bioconductor.org/p/81098/, I can see that there might be some issues with the argument 'bwa ...
medips R bwa medip-seq written 15 months ago by stb0 • updated 15 months ago by Lukas Chavez470

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