User: Lillyhchen

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

Posts by Lillyhchen

<prev • 25 results • page 2 of 3 • next >
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Comment: C: Running DESeqDataSet with 4 factors?
... Thanks! that helped a lot, i didn't notice I didn't specify the column from se and changed the code to colData(se)$Cell and the rest of the DESeq ran perfectly without any errors!  I contrasted the A1 vs A2 and B1 vs B2 and filtered out the results based on padj and log2FoldChange and found 1330 di ...
written 4.2 years ago by Lillyhchen10
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Comment: C: Running DESeqDataSet with 4 factors?
... Hi,  Thanks for answering, does it matter if the factors are grouped together in the colData for the summarizedExperiment or should it be done with after the dds pipeline is run?   I combined the 2 factors as a column in the se: colData(se)$Cell_Treat<-factor(paste0(colData$Cell, "-", colData ...
written 4.2 years ago by Lillyhchen10 • updated 4.2 years ago by Michael Love25k
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Running DESeqDataSet with 4 factors?
... Hello, I'm currently working on a project with two tumor cell lines each from a different patient, and each one of the tumor cell lines has a control and treated group.  I'm trying to look at the changes in gene expression that occur in each tumor cell line between untreated and those treated with ...
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Comment: C: Getting different results with DESeq2
... Sorry for the confusion, but yes that's what I'm working with. Basically, I have two tumor cell lines each from a different patient, and each one of the tumor cell lines has a control and treated group, so as you were saying that would be 4 groups all together when I created a .csv file with both tu ...
written 4.2 years ago by Lillyhchen10
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Getting different results with DESeq2
... Hi I'm having an issue with DESeq2 results.  I'm working with 2 cell lines from different patients and originally I created a .csv excel file with both cell lines in it and then contrasted the results from the DESEq Analysis: setwd("C:/Users/lchen/Documents/transfer.lilly/TMZ.052215") sample=read.c ...
deseq2 rstudio results written 4.2 years ago by Lillyhchen10 • updated 4.2 years ago by Michael Love25k
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Comment: C: SummarizeOverlaps in R
... Hi valerie, I played around with it this morning and it worked! I ended up checking my file names, restarted R, and used serialParam instead of snow! Thanks for all your help :) Lilly ...
written 4.3 years ago by Lillyhchen10
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Comment: C: SummarizeOverlaps in R
... Also, when i looked at summarizeOverlaps I get these warning messages: > summarizeOverlaps() Error in (function (classes, fdef, mtable)  :    unable to find an inherited method for function ‘summarizeOverlaps’ for signature ‘"missing", "missing"’ In addition: Warning messages: 1: In read.dcf(fil ...
written 4.3 years ago by Lillyhchen10
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Comment: C: SummarizeOverlaps in R
... I just tried running my own script and got this error instead: > se <- summarizeOverlaps(features=exons, reads=list, +                         mode="Union", +                         singleEnd=FALSE, +                         ignore.strand=FALSE, +                         fragments=TRUE) Err ...
written 4.3 years ago by Lillyhchen10
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Comment: C: SummarizeOverlaps in R
... Yes that code works: > library(pasillaBamSubset) > library(TxDb.Dmelanogaster.UCSC.dm3.ensGene) > exons <- exonsBy(TxDb.Dmelanogaster.UCSC.dm3.ensGene, "gene") >  > bf <- BamFile(untreated1_chr4(), yieldSize=50000) >  > se <- summarizeOverlaps(exons, bf, BPPARAM = Seri ...
written 4.3 years ago by Lillyhchen10
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Comment: C: SummarizeOverlaps in R
... I never thought about the port being blocked, I think that might be the problem!  SerialParam ran and gave me results: > library(BiocParallel) > bplapply(1:2, function(i) { Sys.sleep(1); i }, BPPARAM=SerialParam()) [[1]] [1] 1 [[2]] [1] 2 And when i run SnowParam, i get the same error mess ...
written 4.3 years ago by Lillyhchen10

Latest awards to Lillyhchen

Popular Question 4.2 years ago, created a question with more than 1,000 views. For Getting different results with DESeq2
Popular Question 4.2 years ago, created a question with more than 1,000 views. For is AClust package still available?
Popular Question 4.2 years ago, created a question with more than 1,000 views. For makeTxdbfromUCSC Warning message
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Running DESeqDataSet with 4 factors?
Popular Question 4.2 years ago, created a question with more than 1,000 views. For DESeqDataSet 2 factors with a covariate
Popular Question 4.2 years ago, created a question with more than 1,000 views. For DESeqDataSet 2 factors with a covariate

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