User: tptacek3050

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Posts by tptacek3050

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Comment: C: MEDIPS vs MACS: why does MEDIPS generate more conservative p-values
... The minRowSum parameter appears to be working. I still haven't gotten it to the level where I'm getting the number of hits MACS was returning (I need to see what kind of parameters they were using for MACS as well), but adjusting it yielded immediate results.   I had built my scripts using a MEDIP ...
written 4.0 years ago by tptacek30500
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MEDIPS vs MACS: why does MEDIPS generate more conservative p-values
... I'm working on getting MEDIPS running for some collaborators who previously had been using MACS to analyze their methyl cap seq data.   I've run MEDIPS on a data set that they had previously run through MACS. I only got one solid hit (p<0.05 after correction for multiple comparisons) using MEDI ...
medips p-value macs written 4.0 years ago by tptacek30500 • updated 4.0 years ago by Lukas Chavez510
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Comment: C: MEDIPS: Any way to get more columns/data from MEDIPS.mergeFrames?
... I decided to go ahead and write a bash script to compile the data. I also went with minimum p-value instead of averaging (I know its not valid ... we were just looking for a way to attach some measure of significance to the merged interval).   Thanks for the feedback anyway. I may try using the me ...
written 4.1 years ago by tptacek30500
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MEDIPS: Any way to get more columns/data from MEDIPS.mergeFrames?
... I didn't see this in the documentation so I thought I'd ask here.   I was wondering whether there was any way to get more data about the merged regions from MEDIPS.mergeFrames. Specifically, I was thinking about pValue, absolute counts, rpkm, and log2FC. I'm assuming that these would be average va ...
medips mergeframes written 4.1 years ago by tptacek30500 • updated 4.1 years ago by Lukas Chavez510
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Comment: C: MEDIPS: Output appears to be truncated
... write.table worked!   The output looks right now. Thanks for your help. I'll post a new topic if something else looks off. ...
written 4.2 years ago by tptacek30500
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Comment: C: MEDIPS: Output appears to be truncated
... I tried running again, changing two of the files in each group to match your specifications (- to _, no #s starting the file name), and got the same results. Next I tried running against a smaller data set (3 files in each set) where all of the files have been renamed (- to _, no #s starting the fi ...
written 4.2 years ago by tptacek30500
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Comment: C: MEDIPS: Output appears to be truncated
... Everything appeared to finish with no errors. Here are the contents of the various data structures: files1 [1] "raw_data_test_1/2668-SMC-0001.sort.bam" [2] "raw_data_test_1/2668-SMC-0002.sort.bam" [3] "raw_data_test_1/2668-SMC-0003.sort.bam" [4] "raw_data_test_1/2668-SMC-0004.sort.bam" [5] "raw_d ...
written 4.2 years ago by tptacek30500
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MEDIPS: Output appears to be truncated
... I am attempting to run the latest version of MEDIPS. I have been following the example in this tutorial to set up my R script: http://www.bioconductor.org/packages/2.12/bioc/vignettes/MEDIPS/inst/doc/MEDIPS.pdf Everything runs without any errors, however, the output doesn't look right to me. For ex ...
medips written 4.2 years ago by tptacek30500 • updated 4.2 years ago by Lukas Chavez510

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