Normalize Cel Files And Identify Differentially Expressed Genes (I.E.Down-Regulated) In Tumor Samples

Question

[User 6686]

BioStar Groups

Hi, I would like to identify differentially expressed genes in tumor samples of GSE11024 and later do clustering (k-means) for down-regulated genes. When I tried to boxplot the exprs(eset) there was an error message. Could you help me solving this error. I would be glad and highly appreciate for your kindness.

An error less than x [! Xna]: object of type 'S4' is not subsettable Additional Information: Warning messages:

1: In is.na(x) : is.na() applied to non-(list or vector) of type 'S4' 2: In is.na(x) : is.na() applied to non-(list or vector) of type 'S4' >

Warm regards, Haobijam SNU, Seoul KOREA

[Michael]

You need to post the output of sessionInfo() including version of affy package and the exact command sequence (from library(affy) to the command throwing an error). Otherwise we have no chance of reproducing this. Sending an email to the bioconductor mailing list might be the better choice, but there the same rules for posting a reproducible example apply.

[Michael]

please use the 'edit' link below the question!

[Michael]

Btw.: you simply cannot run boxplot on an eset, why would you do that anyway?

[Michael]

(1) please use the 'edit' link below the question! (2) please use the 'edit' link below the question! (3) please use the 'edit' link below the question! is that so difficult?

Answer 1

[Michael]

try:

example(rma)
boxplot(exprs(eset))

Does it give a plot? If so, something is wrong with your data.