User: Sally

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Sally250
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Posts by Sally

<prev • 25 results • page 1 of 3 • next >
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Adding annotations to fit2 - still having problems
... Hello, I am using Limma for microarray analysis. Ultimately I want to add/combine/append (not sure what word is correct) a file named MGL.txt (mastergene list) to fit2 so that when topTable prints it will have the annotation information for each gene. The first few lines of MGL.txt looks like thi ...
microarray limma written 10.8 years ago by Sally250 • updated 10.8 years ago by Sean Davis21k
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Adding annotations to fit2
... I want merge fit2 with a txt file I'll call MGL (mastergenelist) which contains gene id information. I am using a custom cDNA array. The reason is that I want the gene ID information along-side the rownames (which are the accession IDs). Both have identical row names. MGL has missing data. I ha ...
written 10.8 years ago by Sally250 • updated 10.8 years ago by john seers IFR810
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At what point do you require an FDR: how many tests?
... I have done alot of reading on multiple testing but I don't recall reading what the cut-off for FDR? In other words how many tests can you run before you need an FDR? Sally Goldes [[alternative HTML version deleted]] ...
written 10.8 years ago by Sally250 • updated 10.8 years ago by Sean Davis21k
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Repost of Error Message: Error in dim(data)<-dim: attempt to set an atrribute on NULL
... I have the following code, from which I get the following error message: Error in dim(data) <- dim : attempt to set an attribute on NULL The script works fine until I get to the ------ line below at the end of the data. #Load libraries source("http://bioconductor.org/biocLite.R") biocLite() li ...
written 10.8 years ago by Sally250
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Error: : Error in dim(data) <- dim : attempt to set an attribute on NULL
... I am getting the following error message: Error in dim(data) <- dim : attempt to set an attribute on NULL from the following Limma script (post-pre-processing) #Load libraries source("http://bioconductor.org/biocLite.R") biocLite() library(limma) library(Biobase) #change directory to folder ...
limma written 10.8 years ago by Sally250
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Limma- Filtering After Statistical Analysis
... Hi, I am relatively new to Limma. I want to filter my gene list after my statistical analysis. What object do I filter on (fit2?)? I looked at genefilter and multtest and they both filter on the ExpressionSet. But this occurs before the statistical analysis. Sally Here is my Limma script: #L ...
genefilter multtest limma written 10.8 years ago by Sally250 • updated 10.8 years ago by Gordon Smyth39k
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Limma and post statistical filtering of genes
... Hello, I have used Limma for preprocessing and statistical analysis. I want to filter my gene list after the statistical analysis but before the FDR is applied. My analysis generates the table fit2. The fit2 table has the following headers: Coefficients df.residual sigma stdev.unscaled A mean S ...
preprocessing limma written 10.8 years ago by Sally250
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LIMMA Error Message:Error in new("AnnotatedDataFrame", data = phenotypicdata) : trying to generate an object from a virtual class ("AnnotatedDataFrame")
... Hi, I am using the current version of LIMMA (January 25, 2009) and am having the following error message from this script below: Error Message: Error in new("AnnotatedDataFrame", data = phenotypicdata) : trying to generate an object from a virtual class ("AnnotatedDataFrame") Problematic Script ( ...
limma written 10.9 years ago by Sally250
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Filtering before differential analysis
... Is flagging the same as filtering? In my Limma script it takes only those ESTs with a flag of 0 (which are good spots). myfun <- function(x) as.numeric ( x$Flag >0) Is this not the same as filtering? If I actually remove the absent spots from my Imagene files, then the files each have dif ...
limma written 10.9 years ago by Sally250 • updated 10.9 years ago by Jenny Drnevich1.9k
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Error in getClass(Class, where = topenv(parent.frame())) : "AnnotatedDataFrame" is not a defined class
... I wrote a script for LIMMA about 9 months ago, which worked fine. Today ran it again (I've updated to the current R version) But got the following error message after this script: adf<-new("AnnotatedDataFrame",data=phenotypicdata) Error in getClass(Class, where = topenv(parent.frame())) : "A ...
limma written 10.9 years ago by Sally250

Latest awards to Sally

Popular Question 10.8 years ago, created a question with more than 1,000 views. For Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,

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