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How To Solve The Read.Maimages Error In Limma Package Of R ?

i'm working on agilent data. for the analysis i am using R and bioconductor package limma. in read.maimages RG <-read.maimages(targets$FileName,source="agilent") m getting the following error

Error in file(file, "r") : cannot open the connection In addition: Warning message: In file(file, "r") : cannot open file 'GSM1098484_US10283824_252665211335_S01_GE1_107_Sep09_1_1'

i have set the directory path also i mentioned all the file names in targets.txt

please help with this.

Thank you.

microarray agilent r limma
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updated by Biostar Biostar • written by Arpitha Hebbar Arpitha Hebbar

what is the output of 

targets$FileName[!file.exists(targets$FileName)]

?

• 96 views • link
written by brentp brentp

it read the file very thankfull to u.

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written by Arpitha Hebbar Arpitha Hebbar

I'd guess that the file indeed does not exist or cannot be opened for another reason, as the error message states, try the code from brent please, that's a good way to check for this mistake.

• 146 views • link
written by Michael Dondrup Michael Dondrup

closed as no longer relevant, it is obviously not an error in limma but a wrong configuration and op didn't attend the question.

• 0 views • link
written by Michael Dondrup Michael Dondrup

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