Question

GEOquery and Feature data

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Entering edit mode

ekl • 0

@ekl-22229

Last seen 6.0 years ago

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"),
               keytype = "PROBEID")

Thank you in advance. Also how do I use the read.table function to put a txt file into R?

GEOquery featureNames • 1.6k views

ADD COMMENT • link updated 6.0 years ago by Sean Davis 21k • written 6.0 years ago by ekl • 0

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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?

ADD REPLY • link 6.0 years ago ekl • 0

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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: unexpected '>' in ">"
> z<-getGEO("GPL8345")
File stored at: 
C:\Users\EKL\AppData\Local\Temp\RtmpaWAMqb/GPL8345.soft
Warning: 9727 parsing failures.
  row     col           expected             actual         file
12956 SPOT_ID 1/0/T/F/TRUE/FALSE 18s_rRNA: Zea mays literal data
12957 SPOT_ID 1/0/T/F/TRUE/FALSE 18s_rRNA: Zea mays literal data
12958 SPOT_ID 1/0/T/F/TRUE/FALSE 18s_rRNA: Zea mays literal data
12959 SPOT_ID 1/0/T/F/TRUE/FALSE 20192.m00001_at    literal data
12960 SPOT_ID 1/0/T/F/TRUE/FALSE 20192.m00002_at    literal data
..... ....... .................. .................. ............
See problems(...) for more details.

> head(Table(z))
              ID    CLONE_ID
1 1569.m00638_at AFLA_000010
2 1569.m00637_at AFLA_000020
3 1569.m00636_at AFLA_000330
4 1569.m00635_at AFLA_000340
5 1569.m00634_at AFLA_000350
6 1569.m00633_at AFLA_000360
                                                  Description
1                              conserved hypothetical protein
2                        penicillin-binding protein, putative
3 multiple ankyrin repeats single kh domain protein, putative
4                         short-chain dehydrogenase, putative
5               NAD dependent epimerase/dehydratase, putative
6                                        hypothetical protein
                                        GO terms             Interpro SPOT_ID
1                                                                          NA
2                                     GO:0046677            IPR001466      NA
3                                                                          NA
4                                                                          NA
5 GO:0003854  GO:0006694  GO:0006808  GO:0016564 IPR002225, IPR008030      NA
6                                                                          NA
> library(GPL8345)
Error in library(GPL8345) : there is no package called ‘GPL8345’
> z<-anno[!is.na(z$SYMBOL),]
Error: object 'anno' not found
> anno<-z[!is.na(anno$SYMBOL),]
Error: object 'anno' not found
> Table(z))<-anno[!is.na(anno$SYMBOL),]
Error: unexpected ')' in "Table(z))"
> Table(z)<-anno[!is.na(anno$SYMBOL),]
Error: object 'anno' not found
> library(GEOquery0
+ anno
Error: unexpected symbol in:
"library(GEOquery0
anno"
> library(GEOquery)
> anno<-select("GEOquery, keys = (featureNames(eset)),
+                columns = c("SYMBOL", "GENENAME"),
Error: unexpected symbol in:
"anno<-select("GEOquery, keys = (featureNames(eset)),
               columns = c("SYMBOL"
>                keytype = "PROBEID")
Error: unexpected ')' in "               keytype = "PROBEID")"
> anno<-select(GEOquery, keys = (featureNames(eset)),
+                columns = c("SYMBOL", "GENENAME"),
+                keytype = "PROBEID")

ADD REPLY • link updated 6.0 years ago by Martin Morgan 25k • written 6.0 years ago by ekl • 0

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Entering edit mode

In your select above, you'll need to use an Annotation database, not GEOquery. You also seem to have a fair number of typos, so you may benefit from a little instruction in using R, as having a foundation in the basics or R is valuable for using Bioconductor.

ADD REPLY • link 6.0 years ago Sean Davis 21k