Question

read.maimages(targets, source="genepix") Error in `[.data.frame`(obj, , columns[[a]]) : undefined columns selected

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sankhwar.madhu • 0

@sankhwarmadhu-13035

Last seen 7.6 years ago

Hi bioconductor help

I am Madhuand trying to analyze the breast cancer data of sereis GSE9893 which is having gpr file as one channel microarray and data counted as median Transformed log. Images have been analyzed using GenePIx. I must be sure there is a problem in making targets.txt file however I made it as suggested in limma package but maimge function is shwoing error. Could you suggest how to make target file for this series.

Error in `[.data.frame`(obj, , columns[[a]]) : undefined columns selected.

could you help me to resolve the problem

FileName   Target
GSM249296.gpr   R
GSM249524.gpr   RF
GSM249527.gpr   R
GSM249529.gpr   R
GSM249530.gpr   RF
GSM249531.gpr   R
GSM249532.gpr   R
GSM249533.gpr   RF
GSM249534.gpr   RF
GSM249535.gpr   RF
GSM249536.gpr   R
GSM249537.gpr   R

bioconductor limma agilent microarrays • 1.9k views

ADD COMMENT • link updated 7.6 years ago by James W. MacDonald 67k • written 7.6 years ago by sankhwar.madhu • 0

score 0 · Answer 1 · 2017-05-15

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 4 days ago

United States

The arrays used for that experiment were custom one-color arrays, so you have to specify the columns by hand:

> z <- read.maimages(dir(".", "^GSM"), columns = list(R = "F635 Median", Rb = "B635 Median"))

Read GSM249296.gpr.gz
Read GSM249524.gpr.gz
Read GSM249527.gpr.gz
Read GSM249529.gpr.gz
Read GSM249530.gpr.gz
Read GSM249531.gpr.gz
Read GSM249532.gpr.gz
Read GSM249533.gpr.gz
<snip>
Read GSM250016.gpr.gz
Read GSM250017.gpr.gz
Read GSM250018.gpr.gz
exiting from: read.maimages(dir(".", "^GSM"), columns = list(R = "F635 Median",
    Rb = "B635 Median"))
>

ADD COMMENT • link 7.6 years ago James W. MacDonald 67k

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Dear james,

Thank you for giving me quick reply

I am naive in bioconductor. I just ran the code which you have provided. again it is showing the error.

z <- read.maimages(dir(".", "^GSM"), columns = list(R = "F635 Median", Rb = "B635 Median"))
Read GSM249524.gpr 
Read GSM250016.gpr 
Error in readGenericHeader(fullname, columns = columns) : 
  Specified column headings not found in file
In addition: There were 50 or more warnings (use warnings() to see the first 50)

>

ADD REPLY • link 7.6 years ago sankhwar.madhu • 0