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I'm filtering the gene expression value of a particular gene using Bioconductor in R. Following the instruction given here, 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?

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  • $\begingroup$ Welcome to the site. First, is your matrix a matrix of numbers or it has text too? Second in the Meta(gds3782) is there any column describing this or not? (It should but I don't know how it is named in this case). You need only to locate the column $\endgroup$ – llrs Aug 13 '18 at 15:53
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You're looking for the Columns() function:

> Columns(gds3782)
     sample        disease.state           description
1  GSM524151 non-diabetic control  Value for GSM524151: beta-cells_non-diabetic condition_donor1; src: human beta-cells_non-diabetic
2  GSM524152 non-diabetic control  Value for GSM524152: beta-cells_non-diabetic condition_donor2; src: human beta-cells_non-diabetic

Note that it's probably easier to work with a more common structure like and expressionSet:

eset = GDS2eSet(gds3782)

You'd then use the pData() function to return the same thing.

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