User: cfreije

gravatar for cfreije
cfreije10
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New User
Location:
United States
Last seen:
2 years, 6 months ago
Joined:
3 years, 2 months ago
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c******@rockefeller.edu

Posts by cfreije

<prev • 9 results • page 1 of 1 • next >
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Comment: C: barcode plot function in limma
... Thank you so much! Loading limma by itself allowed the code to complete without error.   ...
written 2.5 years ago by cfreije10
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barcode plot function in limma
... Dear bioconductor support, I am trying use barcodeplot to visualize gene set enrichment using limma's function barcode plot. I am feeding the function a vector of the t-statistics from the fit2 object with the column indicating the contrast of interest, and the index is a vector of the indices that ...
limma gene set analysis barcodeplot written 2.5 years ago by cfreije10 • updated 2.5 years ago by Gordon Smyth32k
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Comment: C: RNAseq multifactor experiment limma design with patient and batch effects
... Aaron, Thank you for your quick and helpful post. Regarding the first approach you mentioned (including batch in the design and then blocking for patientID using duplicate correlation), I forgot to mention in my first post a limitation of our samples. We have one batch that only has samples for on ...
written 3.1 years ago by cfreije10
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RNAseq multifactor experiment limma design with patient and batch effects
... I have a question regarding the design matrix set up for a multifactor time course RNASeq experiment. My experiment is made up of 12 patients, the patients have one of two diseases A or B (6 A patients, 6 B patients), and each patient has samples at 4 time points (1, 2, 3, and 4). For unavoidable r ...
rnaseq batcheffect limma written 3.1 years ago by cfreije10 • updated 2.5 years ago by robert.maughan0
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Comment: C: Error in simpleLoess when running DEXSeq
... Martin, Thanks again for your help. That worked great! cfreije ...
written 3.1 years ago by cfreije10
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Comment: C: Error in simpleLoess when running DEXSeq
... Martin, Thank you for your help. Following your instructions, I installed and loaded the developmental version of DEXSeq: > library(BiocInstaller) > useDevel() > biocLite("DEXSeq") > library(DEXSeq) However, when I make the DEXSeq count data set I get the following error: >  dsds ...
written 3.2 years ago by cfreije10
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Comment: C: Error in simpleLoess when running DEXSeq
... Just to follow up, I am attempting to use the development version of DEXSeq (version 1.11.14). I used the commands provided on the DEXSeq developmental version bioconductor page (http://bioconductor.jp/packages/3.0/bioc/html/DEXSeq.html) : > source("http://bioconductor.org/biocLite.R") > bio ...
written 3.2 years ago by cfreije10
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Comment: C: Error in simpleLoess when running DEXSeq
... Thank you for your help Alejandro. I just want to check before I attempt to run this again. The development version of DEXSeq would be version 1.11.14? ...
written 3.2 years ago by cfreije10
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Error in simpleLoess when running DEXSeq
... I am attempting to run DEXSeq on an RNASeq data set to determine if there is differential splicing due to treatment condition. However, during the estimate dispersions step I get the following error: simpleLoess(y, x, w, span, degree, parametric, drop.square, normalize, : NA/NaN/Inf in foreign funct ...
rnaseq error dex simpleloess written 3.2 years ago by cfreije10 • updated 3.2 years ago by Alejandro Reyes1.5k

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For RNAseq multifactor experiment limma design with patient and batch effects

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