User: mnaymik

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mnaymik10
Reputation:
10
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New User
Location:
United States
Last seen:
1 month ago
Joined:
2 years, 9 months ago
Email:
m******@asu.edu

Posts by mnaymik

<prev • 21 results • page 1 of 3 • next >
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Ensemble Biomart no human?
... Did the human data set name change? I can't find it al all under listDatasets() either.   EDIT Reinstalling biomart fixed it for me. A colleague of mine had the same issue so not sure what caused it... ...
biomarrt written 4 weeks ago by mnaymik10 • updated 4 weeks ago by Mike Smith2.2k
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FEM Errors out after Monte Carlo Runs
... What exactly does this error mean? Are there some parameters I can change to avoid this?   Error in sgcN.lo[[selMod.idx[m]]] :    attempt to select less than one element   ...
fem written 9 months ago by mnaymik10
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SCDE for differential expression
... I really like the approach taken in the SCDE package for single cell differential expression. In the examples differential expression analysis is performed between two cell types but would it be appropriate to use this package for differential expression in other scenarios? For example, all cell typ ...
differential expression single cell scde written 17 months ago by mnaymik10
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Comment: C: edgeR subsetting DGEList by column/sample
... Since I was using the time column as my group I had set the samples$group=NULL. Later I had been setting group = time which if I do before subsetting It works just fine. I did not realize group was that sensitive. Thanks! ...
written 18 months ago by mnaymik10
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Comment: C: edgeR subsetting DGEList by column/sample
... > library(edgeR) Loading required package: limma > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.5 (El Capitan)   locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8   attached base packages: [ ...
written 18 months ago by mnaymik10
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edgeR subsetting DGEList by column/sample
... I saw this post from a while ago regarding a similar issue: https://support.bioconductor.org/p/61016/ >d$samples[1:6,] sample                                                   lib.size    norm.factor  type    time preExercise_TAGGCTGACTTGAG.1      856    1.1020236     B  pre preExercise_TCCATC ...
edger dgelist subsetting written 18 months ago by mnaymik10 • updated 18 months ago by Gordon Smyth32k
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Comment: C: Using Scran normalization with in edgeR
... Yeah, I noticed that the change is very small. I went through the differential expression workflow in edgeR on the same dataset ordered differently and the results are almost identical. Thanks again for the help! ...
written 18 months ago by mnaymik10
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Comment: C: Using Scran normalization with in edgeR
... I noticed also that if I change the order or the samples in the data frame and normalize via the quick cluster method that the size factors slightly change. Is there a random seed or something that is causing this? ...
written 18 months ago by mnaymik10
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Comment: C: how to get normalized counts from edgeR
... By this method are the new 'nc' table values in counts per million? ...
written 18 months ago by mnaymik10
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Comment: C: Using Scran normalization with in edgeR
... Thank you very much! ...
written 18 months ago by mnaymik10

Latest awards to mnaymik

Scholar 2.7 years ago, created an answer that has been accepted. For A: BiSeq trimClusters FDR.loc confusion

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