User: Lillyhchen

gravatar for Lillyhchen
Lillyhchen10
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10
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New User
Location:
United States
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2 years, 3 months ago
Joined:
2 years, 4 months ago
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L*********@gmail.com

Posts by Lillyhchen

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makeTxdbfromUCSC Warning message
... Hi everyone, I'm trying to use the makeTxdbfromUCSC() function to create a txdb of exons sorted by genes.  It seems the function runs fine, but I just noticed that when I run the function I get a warning message: "Warning message: In .extractCdsLocsFromUCSCTxTable(ucsc_txtable, exon_locs) :   UCSC ...
genomicfeatures maketxdcfromucsc warning written 2.3 years ago by Lillyhchen10 • updated 2.3 years ago by Marc Carlson7.2k
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Comment: C: DESeqDataSet 2 factors with a covariate
... Thanks! I ended up figuring it out, i think i was getting confused by levels and resultsNames()  and got them mixed up. Thanks again for the help! ...
written 2.3 years ago by Lillyhchen10
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Comment: C: DESeqDataSet 2 factors with a covariate
... Hi, thanks for the suggestion, I've tried to ask a statistician at my institute before, but turns out she doesn't use R for her work.  One of my biggest issues I believe is understanding the design, if I use the design MGMT*Treat is it any different from using MGMT:Treat or MGMT + Treat and in what ...
written 2.3 years ago by Lillyhchen10
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Comment: C: DESeqDataSet 2 factors with a covariate
... Yes, that makes sense.  I've been reading through forum posts and the vignette on interaction terms and it's cleared up a few things for me.  Currently I'm using:  > dds<-DESeqDataSet(se, design=~MGMT*Treat) > dds$Treat<-relevel(dds$Treat,"untrt") > dds<-DESeq(dds)   From what ...
written 2.3 years ago by Lillyhchen10
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Comment: C: DESeqDataSet 2 factors with a covariate
... Okay that's what I thought, but I wasn't sure if I had done something else wrong.  I ended up removing the Cell column and now I'm left with 2 factors, MGMT and Treatment.  My current design is ~Treat_MGMT with the two factors combined into a group and I am trying to contrast the untrt vs the trt fo ...
written 2.3 years ago by Lillyhchen10
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Comment: C: DESeqDataSet 2 factors with a covariate
... Oh okay thanks! I see what you're saying, I converted MGMT to a integer value as "1" and "0" instead of "pos" and "neg", but I still get the same error when I run DESeqDataSet.   > colData(se) DataFrame with 12 rows and 5 columns sample Cell Treat MGMT Ce ...
written 2.3 years ago by Lillyhchen10
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DESeqDataSet 2 factors with a covariate
... Hello, I'm running DESeq with the design=~Cell_Treat + MGMT.  I'm working with 6 samples from two different patients, so 12 samples in total.  There are two factors, Cell line (HF2303 or HF 2927) and Treatment (untrt or trt).  I'm trying to include a continuous covariate into the design (MGMT) to c ...
deseq2 covariate multiple factor design deseqdataset written 2.3 years ago by Lillyhchen10 • updated 2.3 years ago by Michael Love14k
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Comment: C: is AClust package still available?
... I get the same error message when I run that code > devtools::install_github("PeteHaitch/Aclust", dependencies=TRUE) Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :    there is no package called ‘Rcpp’ When I run loadNamespace("Rcpp"), it still says it ...
written 2.3 years ago by Lillyhchen10
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Comment: C: is AClust package still available?
... Hi, thanks for answering, and yes that is the Aclust file from Pete Haitch I was talking about.  I didn't know R could download from github but after looking a few things up I found this code: install.packages("devtools") devtools::install_github("username/packagename") I tried to install the pac ...
written 2.3 years ago by Lillyhchen10
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is AClust package still available?
... Hi everyone, I have a list of files that I am trying to cluster hypermethylated genes into cluster sites based on their distance from each other.  I've read about a package called "AClust" for R that would allow me to annotate and cluster genes into specific regions.  However, I can't seem to find ...
rstudio aclust aclustering clusters written 2.3 years ago by Lillyhchen10 • updated 2.3 years ago by Nitish Kumar Mishra30

Latest awards to Lillyhchen

Popular Question 2.3 years ago, created a question with more than 1,000 views. For Running DESeqDataSet with 4 factors?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For DESeqDataSet 2 factors with a covariate
Popular Question 2.3 years ago, created a question with more than 1,000 views. For DESeqDataSet 2 factors with a covariate

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