Error in a method
1
0
Entering edit mode
@tanujadas55-8209
Last seen 8.9 years ago
United States
library(Biobase)
library(GEOquery)
library(simpleaffy)

gds4758 <- getGEO('GDS4758',"GDS4758.soft")
eset <- GDS2eSet(gds4758, do.log2=TRUE)
sampleNames(eset)
 [1] "GSM907858" "GSM907859" "GSM907860" "GSM907854" "GSM907855" "GSM907856"
 [7] "GSM907857" "GSM907825" "GSM907828" "GSM907832" "GSM907833" "GSM907834"
[13] "GSM907826" "GSM907827" "GSM907829" "GSM907830" "GSM907831" "GSM907792"
[19] "GSM907795" "GSM907801" "GSM907802" "GSM907804" "GSM907805" "GSM907806"
[25] "GSM907793" "GSM907794" "GSM907796" "GSM907797" "GSM907798" "GSM907799"
[31] "GSM907800" "GSM907803" "GSM907864" "GSM907865" "GSM907868" "GSM907869"
[37] "GSM907870" "GSM907861" "GSM907862" "GSM907863" "GSM907866" "GSM907867"
[43] "GSM907839" "GSM907840" "GSM907842" "GSM907843" "GSM907845" "GSM907846"
[49] "GSM907848" "GSM907851" "GSM907835" "GSM907836" "GSM907837" "GSM907838"
[55] "GSM907841" "GSM907844" "GSM907847" "GSM907849" "GSM907850" "GSM907852"
[61] "GSM907853" "GSM907807" "GSM907813" "GSM907814" "GSM907816" "GSM907818"
[67] "GSM907819" "GSM907820" "GSM907822" "GSM907823" "GSM907808" "GSM907809"
[73] "GSM907810" "GSM907811" "GSM907812" "GSM907815" "GSM907817" "GSM907821"
[79] "GSM907824"

geneNames(eset)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘geneNames’ for signature ‘"ExpressionSet"’

Please help me with this error ! The dataset i used here is that of alzheimer disease.

affy • 682 views
ADD COMMENT
1
Entering edit mode
@james-w-macdonald-5106
Last seen just now
United States

There isn't a geneNames() function for ExpressionSets any longer. There is a featureNames() function, which will give you the manufacturer's ID for each reporter on the array. But I suspect that isn't what you want. If you want the HUGO gene symbol, then you need an annotation package for this array.

These appear to be Human Gene 1.0 ST arrays from Affymetrix, and the submitter says this about the processing:

"CEL files were imported into Affymetrix Expression Console Software, and CHP files were generated."

Which is like, helpful and stuff, so let's assume they summarized at the transcript (or core) level, so you want to annotate using the hugene10sttranscriptcluster.db package. See the vignette(s) for AnnotationDbi for more information about how to accomplish that.

You can check to see if the data are summarized at the core level by doing something like

all(featureNames(eset) %in% keys(hugene10sttranscriptcluster.db))

after installing and loading the hugene10sttranscriptcluster.db package, of course.

ADD COMMENT

Login before adding your answer.

Traffic: 943 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6