Error in groups
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Entering edit mode
5.3 years ago
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Hi I was working on GSE38642 and got an error in defining phenotypic data while making groups for analyzing differential expression. I think I've defined groups properly but still getting error and it is as follows:

> groups = pData(phenoData(gse38642dat[[1]]))$status > groups=as.character(groups) > groups[groups=="non-diabetic donors"]="control" > groups[groups=="T2D donors"]="T2D" > f = factor(groups, levels=c("control","T2D")) > f [1] <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> [16] <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> [31] <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> [46] <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> [61] <NA> <NA> <NA> Levels: control T2D  Why it isn't recognizing the samples?Please help me in finding error. It'll be very helpful for me. R affy limma GEOquery phenotypic Data • 1.2k views ADD COMMENT 1 Entering edit mode 5.3 years ago The column that contains the information you want is accessed using: groups = pData(gse38642dat[[1]])$characteristics_ch1.5


Then, you'll need to make some small changes to your code, but that should get you started.

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thank u so much it worked :)