## User: Lillyhchen

Lillyhchen10
Reputation:
10
Status:
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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... Thanks! that helped a lot, i didn't notice I didn't specify the column from se and changed the code to colData(se)$Cell and the rest of the DESeq ran perfectly without any errors! I contrasted the A1 vs A2 and B1 vs B2 and filtered out the results based on padj and log2FoldChange and found 1330 di ... written 4.2 years ago by Lillyhchen10 1 answer 2.4k views 1 answers ... Hi, Thanks for answering, does it matter if the factors are grouped together in the colData for the summarizedExperiment or should it be done with after the dds pipeline is run? I combined the 2 factors as a column in the se: colData(se)$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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... 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 ...
written 4.2 years ago by Lillyhchen10
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... 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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... 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 ...
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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