User: cafelumiere12

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Posts by cafelumiere12

<prev • 18 results • page 2 of 2 • next >
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edgeR in a situation with unbalanced design: to include only subjects with matching time points or not?
... Edited the original question to make it a little clearer: I have a gene expression data set of 165 samples and different subject/ Time-point at which the sample was collected ( after a certain dose of drug and days), source of sample, whether it was CD33/34 enriched or not.  A subset of this actua ...
edger differential gene expression written 2.1 years ago by cafelumiere1220 • updated 2.0 years ago by Gordon Smyth38k
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Comment: C: genefilter filtered out 60% of the original genes?
... Thanks for the comment. Your rephrasing is exactly right; however, the function I wrote was really simply a wrapper based on the manual of genefilter. The only customized functionality I added was the option to do the manual filtering. And this was option was not used in the example .I am not lookin ...
written 3.3 years ago by cafelumiere1220
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Comment: C: genefilter filtered out 60% of the original genes?
... Thanks! Just edited the question and attached the code I used. ...
written 3.3 years ago by cafelumiere1220
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genefilter filtered out 60% of the original genes?
... I'm using edgeR + genefilter. I have used it for a few different projects already but for this one I'm getting a chosen theta = 0.6. I wonder if this is something that I need to be concerned of? It just feels like a lot of genes! Session Info here: sessionInfo() R version 3.2.5 (2016-04-14) Platf ...
genefilter edger written 3.3 years ago by cafelumiere1220 • updated 3.3 years ago by Nikos Ignatiadis160
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Comment: C: edgeR: shall I fit the glm model separately for different cell lines?
... Thank you so much! This is super helpful. Good point about the unnecessary complications there - it was sort of copy paste from my previous project where the contrasts were a lot more complicated & should have changed it. Thanks a lot!!    ...
written 3.3 years ago by cafelumiere1220
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edgeR: shall I fit the glm model separately for different cell lines?
... i all, I have RNAseq data for treated and untreated samples (in triplicates)  in three different cell lines: KO1, KO2, WT. The goal is to do three comparisons: (1) KO1 treated vs. untreated (2) KO2 treated vs. untreated and (3) WT treated vs untreated Here is the group information in a data.frame ...
edger written 3.3 years ago by cafelumiere1220 • updated 3.3 years ago by Ryan C. Thompson7.3k
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exomeCopy copy number setting
... Hello, I have been using exomeCopy with no problem; however I was wondering if anyone has any insight about setting the possible copy number while running the exomeCopy function to get CNVs? I have trid both S=1:4 or 1:6 but I'm not sure if there is a general rule for this. Can I set 1:4 only? Do I ...
exomecopy cnv written 3.7 years ago by cafelumiere1220 • updated 3.7 years ago by Michael Love25k
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Trouble following the first 5 lines of vanillaICE tutorial?
... Dear All, I am trying to analyze CNV from SNP6 data. I've run through crlmm and now trying vanillaICE. At the moment I am just following the exact same lines listed on the vanillaICE tutorial (http://www.bioconductor.org/packages/release/bioc/vignettes/VanillaICE/inst/doc/crlmmDownstream.pdf) And ...
vanillaice crlmm vanillaice crlmm cnv snp6 written 4.3 years ago by cafelumiere1220 • updated 4.3 years ago by rscharpf0

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