Problems with clustering a micro array data using R
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yalaman2 • 0
@yalaman2-8923
Last seen 7.4 years ago
United States

HI

I  am trying to cluster micro array Data with R. 

My micro array data looks like follows 

 

GENE    x    y    Control-sig    Control-bkg    Target-sig    Target-bkg
  JW0001    1    1    14232.93    9737.275    1483.534    974.2833
  JW0001    2    1    15313.71    10535.87    2841.966    733.7246
  JW0002    3    1    10430.46    9633.33    1038.335    985.465
  JW0002    4    1    10890.26    10780.89    1012.796     843.06
  JW0003    5    1    10355.28    9795.589    1206.075    689.7129
  JW0003    6    1    13467.12    12531.38    2381.804    1444.176
  JW0004    7    1    11979.2    11940.02    1488.868    1492.676
  JW0004    8    1    9697.542    9038.31    762.8133    748.7342
  JW0005    9    1    10117.86    9885.01    1002.254    724.0625
  JW0005    10    1    12523.93    12023.07    1646.924    1555.863

 

I obtained it from Kegg database. 

I am trying the following commands in R

library(limma)

targets<-readTargets("filename.txt")

RG<-read.maimages(targets,columns=list(R="Control-sig",G="Target-sig")

 

It is showing me the follwoing error. 

"

Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") : cannot open file '  JW0001': No such file or directory"

 

I have a feeling that I am doing some thing very wrong. I am very new to R. please help.

microarray R clustering • 653 views
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Entering edit mode
arfranco ▴ 130
@arfranco-8341
Last seen 20 hours ago
European Union

You don't provide with enough details

In targets, you define (I hope) the file JW0001 and some other files (I hope again..)

JW0001 is not found in the current directory. Within read.maimages you can define source = , where you can indicate the source of your files

In addition.. With read.maimages you must provide the name of a microarray whole file, not the name of the genes. From the data you provide, JW0001 is the name of one of the many genes you have. I believe with that you have badly defined filenames.txt

Where do you have your files ?

What is the content of targets ?

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