Filtering the expression values of a gene from GEO
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mahm ▴ 20
@mahm-16884
Last seen 5.5 years ago

I'm filtering the gene expression value of a particular gene using Bioconductor in R. Following the instruction given [here][1], I could filter the gene expression value for a gene from the dataset GDS3782. 

The output is as follows for the gene of my interest,

    GSM524151  "23.82"          
    GSM524152  "27.49"          
    GSM524153  "24.26"          
    GSM524154  "17.98"          
    GSM524155  "25.87"          
    GSM524156  "26.16"          
    GSM524157  "26.02"          
    GSM524158  "25"             
    GSM524159  "29.85"          
    GSM524160  "18.25"          
    GSM524161  "28.86"          
    GSM524162  "27.33"          
    GSM524163  "27.42"          
    GSM524164  "28.23"          
    GSM524165  "22.09"          
    GSM524166  "24.85"          
    GSM524167  "27.11"          
    GSM524168  "32.01"          
    GSM524169  "28.97"          
    GSM524170  "30.98" 

The above data corresponds to disease and control which I get using 

    Meta(gds3782)$description

I wish to see the description of each value. For example, from the webpage, I have seen that the first ten values correspond to "disease-state" and the last ten correspond to "control". How do I view this classification while processing the data using Bioconductor in R?
  [1]: https://mdozmorov.github.io/BIOS567/assets/presentation_Bioconductor/GEO.pdf

GEO microarray • 903 views
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What exactly do you mean by 'view this classification while processing the data'? The webpage you link to shows how to use the pData function. Is there something else you want to do?

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By classification I mean, the status description "disease" and "control". i.e. the output that is given when  Meta(gdsxxx)$description is used.

 

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@james-w-macdonald-5106
Last seen 12 hours ago
United States
library(GEOquery)

gse <- getGEO("GSE20966")[[1]]

pData(gse)[,"disease.ch1"]
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