User: Elena Sorokin

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Elena Sorokin150
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Posts by Elena Sorokin

<prev • 15 results • page 1 of 2 • next >
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How to do a Vlookup-type function using a value range
... I have two data frames as input: > small Position 1 6 2 14 3 1 > lookup_table Start Stop Value 1 1 5 a 2 6 10 b 3 11 15 c And I want the following output: > outcome Position Value 1 6 b 2 14 c 3 1 a W ...
written 3.5 years ago by Elena Sorokin150 • updated 3.5 years ago by Harris A. Jaffee590
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RNA-seq analysis and two-way ANOVAs
... Hello, What R packages for differential expression analysis of mRNA-seq data are currently set up to do statistical testing with two main effects (two-way ANOVA)? I know that the latest versions of DESeq and edgeR can do this for genes; I know DEXSeq can do this for exons; I don't think that the l ...
edger bayseq degseq deseq dexseq written 5.2 years ago by Elena Sorokin150 • updated 5.2 years ago by Gordon Smyth32k
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interactions between variables in DEXSeq
... Hello again, I'm writing this time to ask about setting up more complex formulae to test for significant interaction between independent variables in DEXSeq. Using the example from the manual, to test for an interaction between library type and condition, how would I set this up? The syntax here is ...
deseq written 5.4 years ago by Elena Sorokin150 • updated 5.4 years ago by Alejandro Reyes1.5k
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Comment: C: interpreting DEXSeq output
... Hi Alejandro, Yes, the merged genes I find are difficult to interpret - because the differential exon usage is probably just differences in total gene expression. I still wonder about it, because in my mapping procedure, I do a very stringent alignment where reads that map to more than one place in ...
written 5.4 years ago by Elena Sorokin150
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interpreting DEXSeq output
... Hello, How should we be interpreting output from DEXSeq in which some geneIDs within the DEU results table are denoted by multiple genes separated by + signs? I can send examples of what I mean to the developers, if my question is unclear. Especially when the architecture of the two or even three ...
dexseq written 5.4 years ago by Elena Sorokin150 • updated 5.4 years ago by Alejandro Reyes1.5k
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Answer: A: DEXseq: fitDispersionFunction error
... Dear Alejandro, I can't seem to find the development version that you were talking about. I am running the version available for BioC 2.9: http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq.ht ml ...Could you tell me where to download v 1.1.6 of your software? Thanks, Elena On 2 ...
written 5.8 years ago by Elena Sorokin150
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DEXseq: fitDispersionFunction error
... Greetings all, I ran into another problem with the DEXseq program, and I was hoping that somebody could help me once more. :) I successfully ran through a full analysis of one time point of my dataset, and was hoping ideally to extend the analysis to my full time course, using the GLM test. However ...
dexseq written 5.8 years ago by Elena Sorokin150 • updated 5.8 years ago by Alejandro Reyes1.5k
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Comment: C: DEXseq: Making exonCountSet object
... Dear Alejandro and Simon, Thanks, this solved my problem! I am getting actual p-values now. I really appreciate your help. Sincerely, Elena On 2/13/2012 3:29 AM, Alejandro Reyes wrote: > Hi Elena, Thanks for posting the detail email. The p-values and > p-adjusted values should be in your va ...
written 5.8 years ago by Elena Sorokin150
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Answer: A: DEXseq: Making exonCountSet object
... Dear Simon, Thanks for your reply, even on a Saturday. =) You were right about the incorrect file path- that was problem. (To anybody else out there struggling with general issues getting their files into R, my code is below. Hope I save you some time). Another issue I was hoping you might help m ...
written 5.8 years ago by Elena Sorokin150
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DEXseq: Making exonCountSet object
... Hello again, As a result of my recent post, I'm now delving into the DEXseq package. But I am having struggling with building my exonCountSet object, as described in the vignette/ R documentation. First I went through the example in the vignette, and was able to complete the pasilla analysis. With ...
annotation written 5.8 years ago by Elena Sorokin150 • updated 5.8 years ago by Alejandro Reyes30

Latest awards to Elena Sorokin

Popular Question 3.5 years ago, created a question with more than 1,000 views. For RNA-seq analysis and two-way ANOVAs
Popular Question 3.5 years ago, created a question with more than 1,000 views. For RNA-seq analysis and two-way ANOVAs

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