Question: (Closed) How To Solve The Read.Maimages Error In Limma Package Of R ?
0
gravatar for Arpitha Hebbar
4.6 years ago by
India
Arpitha Hebbar170 wrote:

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.

agilent R microarray limma • 2.5k views
ADD COMMENTlink modified 4.3 years ago by Biostar ♦♦ 20 • written 4.6 years ago by Arpitha Hebbar170
1

what is the output of

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

?

ADD REPLYlink written 4.6 years ago by brentp22k

it read the file very thankfull to u.

ADD REPLYlink written 4.6 years ago by Arpitha Hebbar170
1

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.

ADD REPLYlink written 4.6 years ago by Michael Dondrup43k

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

ADD REPLYlink written 4.3 years ago by Michael Dondrup43k
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