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

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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
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updated by Rocky • Rocky • written by User 6686 • User 6686

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.

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written by Michael Dondrup Michael Dondrup

please use the 'edit' link below the question!

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written by Michael Dondrup Michael Dondrup

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

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written by Michael Dondrup Michael Dondrup

(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?

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written by Michael Dondrup Michael Dondrup

2 answers

try:

example(rma)
boxplot(exprs(eset))

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

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written by Michael Dondrup Michael Dondrup

No it does not output a plot. I tried with these comments

library(affy)
setwd("/home/momo/R/R-2.14.1/data/kidney/GSE11024")
rawdata<-ReadAffy()
eset <- expresso(rawdata,normalize.method="quantiles",bgcorrect.method="rma",
                 pmcorrect.method="pmonly",summary.method="liwong")

After processing this numbers of ids
54675 ids to be processed
There were over 50 warning (see warning in warnings () Please use)

Boxplot (eset)

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'
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updated by Neilfws Neilfws • written by Rocky • Rocky

(1) This is not an answer - please edit your original question or use the comments. And don't choose "community wiki". (2) Lines may not display as intended if they start with ">". Preview what you write before posting. (3) Boxplot (eset) is not the command that Michael suggested.

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written by Neilfws Neilfws

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