User: chitsazanalex

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Posts by chitsazanalex

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Mean Expression Calculation scRNA-seq (All cells or only Expressed Cells)
... I'm doing a differential test for monocle and they show that differentialGeneTest() gives the features that are different between your model but doesn't tell you about which specific genes go up for particular groups. Per there documentation, they state "We could also simply compute summary statisti ...
monocle scrnaseq written 4 months ago by chitsazanalex0 • updated 4 months ago by davide risso740
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Comment: C: p-value the same for different contrasts DESeq2
... Gotcha thanks! ...
written 4 months ago by chitsazanalex0
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Comment: C: p-value the same for different contrasts DESeq2
... I did that, as I stated """ From the research that i've done looking into ?results, it seems the contrast parameter stated is used for the logFC calculation and it seems from my googling (and TRYING my best to read stats equations) that the wald test would result in one p-value based on the design ...
written 4 months ago by chitsazanalex0
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p-value the same for different contrasts DESeq2
... I'm confused in regards to the p-value for a multilevel design in deseq2. I have a timecourse (0h, 3h, 6h, 24h) and I want to know what is changing between each pairwise comparison. I'm curious as to how the p-value is the same for individual and all pairwise comparisons (aka 0hvs3h OR 6hvs24h have ...
deseq2 design and contrast matrix written 4 months ago by chitsazanalex0 • updated 4 months ago by Michael Love19k
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Comment: C: Rsubread Installation error
... Yeah that worked. Probably a much better idea. Thanks for the input Alex ...
written 5 months ago by chitsazanalex0
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Comment: C: Rsubread Installation error
... That did not work unfortunately. Still got a very similar error.    [n2232 ~]$ gcc --version gcc (GCC) 6.2.0 Copyright (C) 2016 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PAR ...
written 5 months ago by chitsazanalex0
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Rsubread Installation error
... Hey all, I am getting an error when trying to install Rsubread on our server. Our cluster uses the module system and what's weird is that it only occurs with r_3.3.3 and installs properly with the msropen_3.3.2 version. All of my other packages are loaded with r_3.3.3 though so I want to install it ...
rsubread compilation error written 5 months ago by chitsazanalex0 • updated 5 months ago by Wei Shi2.9k
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Comment: C: DistanceToNearest Not giving nearest Range
... Thank you very much! ...
written 9 months ago by chitsazanalex0
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Comment: C: DistanceToNearest Not giving nearest Range
... I'm doing more than that. It's a function I have that can map any set of ranges to another, not just annotate peaks as it is in this function. Sometimes it's peaks. Sometimes it's an ENCODE dataset, a bed file, etc. I'd more would like to figure out why DistanceToNearest doesn't chose the nearest ra ...
written 9 months ago by chitsazanalex0
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DistanceToNearest Not giving nearest Range
... I'm having trouble why the order of my subject is calling two different nearest cordinates. One is obviously closer, but for some reason it's chosing the first one rather than the actual nearest one. How can I fix this?  Thanks!   Here is my code and a session_info() printout. > ALL_merge ...
granges distancetonearest written 9 months ago by chitsazanalex0 • updated 9 months ago by Julie Zhu3.8k

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