Question: Normalize Cel Files And Identify Differentially Expressed Genes (I.E.Down-Regulated) In Tumor Samples
2
gravatar for User 6686
8.9 years ago by
User 668620
User 668620 wrote:

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

bioconductor affymetrix • 2.2k views
ADD COMMENTlink modified 8.9 years ago by Rocky30 • written 8.9 years ago by User 668620
2

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.

ADD REPLYlink written 8.9 years ago by Michael Dondrup48k
1

please use the 'edit' link below the question!

ADD REPLYlink written 8.9 years ago by Michael Dondrup48k

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

ADD REPLYlink written 8.9 years ago by Michael Dondrup48k

(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?

ADD REPLYlink written 8.9 years ago by Michael Dondrup48k
3
gravatar for Michael Dondrup
8.9 years ago by
Bergen, Norway
Michael Dondrup48k wrote:

try:

example(rma)
boxplot(exprs(eset))

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

ADD COMMENTlink written 8.9 years ago by Michael Dondrup48k
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