User: ekl

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ekl0
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Posts by ekl

<prev • 23 results • page 1 of 3 • next >
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Reading TXT Files
... I am trying to use the read.table function to read a TXT file in R. It says permission denied when I put in the code. What could cause this? ...
read.table txt written 7 days ago by ekl0 • updated 7 days ago by James W. MacDonald51k
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Annotation Packages other than Dbi
... How do I know which annotation package to use when looking at a dataset from GEO NCBI. It is clear that they do not use Annotation Dbi, as the select function does not work. ...
annotation custom written 7 days ago by ekl0 • updated 6 days ago by James W. MacDonald51k
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Annotation Using GEOquery
... I am trying to finish a microarray analysis. The array I am using does not have an annotation package in Bioconductor. I got the data from GEO NCBI. Now I am trying to annotate the data to be able to find DEGs. How do I go about doing that? Also, when I try to use the read.table function for a txt t ...
annotation txt geo written 7 days ago by ekl0 • updated 7 days ago by Sean Davis21k
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Comment: C: GEOquery and Feature data
... here is the code I have gotten so far: library(GEOquery) Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) > > z <- getGEO("GPL8345") Error: unexpected '>' in ">" > > head(Table(z)) Error: unexpec ...
written 7 days ago by ekl0 • updated 7 days ago by Martin Morgan ♦♦ 24k
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Comment: C: Select function not working in R; how to correct custom select
... Okay, then how do I add feature data in order to find differentially expressed genes? ...
written 7 days ago by ekl0
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Comment: C: GEOquery and Feature data
... I am trying to conduct a microarray analysis on a dataset that did not have an annotation package. I added the data into R. How do I proceed with getting probe IDs and differential gene expression? ...
written 7 days ago by ekl0
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GEOquery and Feature data
... Okay, so I added the GEOQuery package and got the data from GEO NCBI. How do I now apply the following step to the data? library("hgu133plus2.db") anno <- select(hgu133plus2.db, keys = (featureNames(eset)), columns = c("SYMBOL", "GENENAME"), ...
geoquery featurenames written 8 days ago by ekl0 • updated 8 days ago by Sean Davis21k
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MEV and TXT files
... I have other articles with datasets in MEV and TXT formats. How do I command R to recognize those formats? Thank you. ...
txt files written 11 days ago by ekl0 • updated 11 days ago by Gordon Smyth39k
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Select function not working in R; how to correct custom select
... I am trying to finish a microarray analysis. I need to select information from the A flavus package to find deferentially expressed genes. Select is not working in Annotation Dbi. How do I create a custom select function so that R recognizes the function? Thank you. cdf=AFLAVUSa520391F (22683 affyi ...
custom select annotation dbi written 11 days ago by ekl0 • updated 11 days ago by James W. MacDonald51k
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Comment: C: Still Not Recognizing CDF
... I think I may have found the problem; I will let you know otherwise. ...
written 13 days ago by ekl0

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