User: Vani

gravatar for Vani
Vani20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
2 years, 1 month ago
Joined:
2 years, 8 months ago
Email:
j*********@yahoo.com

Posts by Vani

<prev • 22 results • page 1 of 3 • next >
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UPC method giving error for Microarray dataset
... Hello, I am trying to normalize a dataset from the Geo site using the SCAN.UPC's UPC method, but it is giving me an error. Here is my code: eset <- UPC("GSE57338") Here is the error: Warning messages: 1: In download.file(file.path(url, i), destfile = file.path(storedir,  :   downloaded le ...
scan.upc upc written 2.2 years ago by Vani20 • updated 2.1 years ago by Stephen Piccolo510
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Comment: C: SCAN.UPC giving error for multiple input files
... Hi Mr.Piccolo, So even if I downloaded the RNA-Seq CEL files and attempted to apply SCAN method, it would not work correct? Also I tried to use the UPC() : normalized <- UPC("GSE46224") And I still got the same error: Error in downloadFromGEO(celFilePattern, expectedFileSuffixPattern = "*.C ...
written 2.5 years ago by Vani20
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SCAN.UPC giving error for multiple input files
... Hi,   I am trying to use SCAN.UPC to normalize a dataset. Whenever I run the command ​normalized = SCAN("GSE46224") I get the error: Error in downloadFromGEO(celFilePattern, expectedFileSuffixPattern = "*.CEL.gz") : No raw data files could be downloaded from GEO for GSE46224​ I checked on ...
scan.upc written 2.5 years ago by Vani20 • updated 2.5 years ago by Stephen Piccolo510
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Error when using write.table() with SCAN.UPC ESET
... Hi,   I am getting an error when I try to save an eset generated by SCAN.UPC  using write.table. Here is my code: gse53080 <- getGEO('GSE53080',GSEMatrix = TRUE) write.table(gse53080, file = "NormalizedGSE53080.txt", sep = "\t")   Here is the error: Error in data.frame(`GSE53080-GPL10999 ...
scan.upc write.table written 2.5 years ago by Vani20
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Comment: C: Problem Installing SCAN.UPC
... It worked with the new version of R (3.2.1)! ...
written 2.6 years ago by Vani20
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Problem Installing SCAN.UPC
... Hi, I am getting errors when I try to install the bioconductor package SCAN.UPC. I am using R version 3.2.0. When I run this command: source("http://bioconductor.org/biocLite.R") biocLite("SCAN.UPC") I get this error: The downloaded source packages are in ‘/tmp/Rtmp7yK0L2/downloaded_packages’ ...
scan.upc installation bioconductor written 2.6 years ago by Vani20
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Meta package metagen() function for multiple datasets
... Hi, I am trying to used the metagen function  to perform a meta-analysis on multiple datasets. In the vignette the data frame for the data parameter, contains one study per line in the dataframe. Is it possible to input multiple data frames at once?  I want to do an comparison on the top ten genes ...
meta metagen written 2.6 years ago by Vani20
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Comment: C: Meta-Analysis after running limma on a normalized dataset
... Hi,  Before I create a forest plot I want to run a fixed and random effect meta-analysis process across all the 4 datasets. I couldn't find a way to do this on rmeta? Do you have any advice in this regard?       ...
written 2.6 years ago by Vani20
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Meta-Analysis after running limma on a normalized dataset
... Hi, I am trying to run a meta-analysis on multiple datasets. After the normalization was completed I applied, limma's lmfit,ebayes, and toptable on the datasets. I would like to use the data produced by toptable to do a meta-analysis on the datasets. This is the header of my top tables:  [1] "ENT ...
limma toptable meta-analysis written 2.6 years ago by Vani20 • updated 2.6 years ago by Aaron Lun18k
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Comment: C: Standard error and effect size from Limma
... Cool thanks. Just a quick question: How would I calculate the standard error from the confidence intervals? ...
written 2.6 years ago by Vani20

Latest awards to Vani

Popular Question 2.1 years ago, created a question with more than 1,000 views. For Creating an Expression Set with a csv file
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimension

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