## User: mnaymik

mnaymik10
Reputation:
10
Status:
New User
Location:
United States
Last seen:
1 year, 8 months ago
Joined:
4 years, 4 months ago
Email:
m******@asu.edu

#### Posts by mnaymik

<prev • 21 results • page 1 of 3 • next >
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... 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... ...
written 20 months ago by mnaymik10 • updated 20 months ago by Mike Smith3.9k
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... 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   ...
written 2.4 years ago by mnaymik10
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611
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... 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 ...
written 3.1 years ago by mnaymik10
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... Since I was using the time column as my group I had set the samples$group=NULL. Later I had been setting group = time which if I do before subsetting It works just fine. I did not realize group was that sensitive. Thanks! ... written 3.1 years ago by mnaymik10 2 answers 2.4k views 2 answers ... > library(edgeR) Loading required package: limma > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.5 (El Capitan) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [ ... written 3.1 years ago by mnaymik10 2 answers 2.4k views 2 answers ... I saw this post from a while ago regarding a similar issue: https://support.bioconductor.org/p/61016/ >d$samples[1:6,] sample                                                   lib.size    norm.factor  type    time preExercise_TAGGCTGACTTGAG.1      856    1.1020236     B  pre preExercise_TCCATC ...
written 3.1 years ago by mnaymik10 • updated 3.1 years ago by Gordon Smyth38k
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... 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 3.1 years ago by mnaymik10
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... 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 3.1 years ago by mnaymik10
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... By this method are the new 'nc' table values in counts per million? ...
written 3.1 years ago by mnaymik10
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911
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... Thank you very much! ...
written 3.1 years ago by mnaymik10

#### Latest awards to mnaymik

Popular Question 20 months ago, created a question with more than 1,000 views. For BiSeq trimClusters FDR.loc confusion
Popular Question 2.4 years ago, created a question with more than 1,000 views. For edgeR subsetting DGEList by column/sample
Scholar 4.3 years ago, created an answer that has been accepted. For A: BiSeq trimClusters FDR.loc confusion

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