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Question: minfi R package for methylation analysis of infinium 450K microarray data
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gravatar for sinha.puja
11 days ago by
sinha.puja0
sinha.puja0 wrote:

Hi,

I was trying to use minfi to read .idat files to get beta values but when I was typing the command 

targets <- read.metharray.sheet("/C:/Users/sinha.puja/Desktop/projectDir/dataDir/revHumanMethylation450_Demo_Sample_Sheet", pattern="Sample_Sheet.csv")

there was error message 

Error in read.metharray.sheet("/C:/Users/sinha.puja/Desktop/baseDir/revHumanMethylation450_Demo_Sample_Sheet",  : 
  'base' does not exists

<font face="monospace">Please help me.</font>

My sample sheet looks like..

Sample_Name Sample_Well Sample_Plate Sample_Group Pool_ID Sentrix_ID Sentrix_Position Basename            
NA17105-M_Rep1 NA NA NA17105-M NA 5.64E+09 R01C01 "/C:/Users/sinha.puja/Desktop/baseDir/5640269011/5640269011_R01C01_.idat"
A431_Rep1 NA NA A431 NA 5.64E+09 R01C02 "/C:/Users/sinha.puja/Desktop/baseDir/5640269011/5640269011_R01C02_.idat"
NA17018-F_Rep1 NA NA NA17018-F NA 5.64E+09 R02C01 "/C:/Users/sinha.puja/Desktop/baseDir/5640269011/5640269011_R02C01_.idat"
MCF7_Rep1 NA NA MCF7 NA 5.64E+09 R02C02 "/C:/Users/sinha.puja/Desktop/baseDir/5640269011/5640269011_R02C02_.idat"
Raji NA NA Raji NA 5.64E+09 R03C01 "/C:/Users/sinha.puja/Desktop/baseDir/5640269011/5640269011_R03C01_.idat"
Hemi-methylated NA NA Hemi-methylated NA 5.64E+09 R03C02 "/C:/Users/sinha.puja/Desktop/baseDir/5640269011/5640269011_R03C02_.idat"
Unmethylated NA NA Unmethylated NA 5.64E+09 R04C01 "/C:/Users/sinha.puja/Desktop/baseDir/5640269011/5640269011_R04C01_.idat"
Methylated NA NA Methylated NA 5.64E+09 R04C02 "/C:/Users/sinha.puja/Desktop/baseDir/5640269011/5640269011_R04C02_.idat"
NA17105-M_Rep2 NA NA NA17105-M NA 5.64E+09 R05C01 "/C:/Users/sinha.puja/Desktop/baseDir/5640269011/5640269011_R05C01_.idat"
A431_Rep2 NA NA A431 NA 5.64E+09 R05C02 "/C:/Users/sinha.puja/Desktop/baseDir/5640269011/5640269011_R05C02_.idat"
NA17018-F_Rep2 NA NA NA17018-F NA 5.64E+09 R06C01 "/C:/Users/sinha.puja/Desktop/baseDir/5640269011/5640269011_R06C01_.idat"
MCF7_Rep2 NA NA MCF7 NA 5.64E+09 R06C02 "/C:/Users/sinha.puja/Desktop/baseDir/5640269011/5640269011_R06C02_.idat"
ADD COMMENTlink modified 11 days ago by James W. MacDonald48k • written 11 days ago by sinha.puja0
0
gravatar for James W. MacDonald
11 days ago by
United States
James W. MacDonald48k wrote:

The first argument to read.metharray.sheet is 'base', and for that you have

"/C:/Users/sinha.puja/Desktop/projectDir/dataDir/revHumanMethylation450_Demo_Sample_Sheet"

Which isn't a directory on Windows (note the preceding forward slash, which is only a thing on Linux and MacOS).

ADD COMMENTlink written 11 days ago by James W. MacDonald48k

I also tried using targets <- read.metharray.sheet(baseDir) but still I got the error 

Error in read.metharray.sheet(baseDir) : 'base' does not exists

I don't know how to resolve this issue. Please help.

ADD REPLYlink written 10 days ago by sinha.puja0

Well I have no idea what baseDir might be, so how could I possibly help? And I already answered your question - perhaps you need to re-read my original answer? And as a hint - remove the extra slash at the beginning of the path to your sample sheet.
 

ADD REPLYlink written 10 days ago by James W. MacDonald48k

After removing the extra slash also I am getting the same type of error i.e,

Error in read.metharray.sheet(baseDir) : 'base' does not exists.

I am stuck at the very first step, don't know how to get rid off. If anyone else is having the same issue or know how to resolve then please respond.

Thanks.

ADD REPLYlink written 10 days ago by sinha.puja0

I keep telling you how to resolve it. The error is telling you that the directory you are pointing to does not exist! If you tell R to read something from a non-existent directory, you shouldn't be surprised if it says that it doesn't exist. As an example:

> dir.does.not.exist <- "C:/this/is/a/fake/directory"
> read.metharray.sheet(dir.does.not.exist)
Error in read.metharray.sheet(dir.does.not.exist) :
  'base' does not exists
> dir.does.exist <- "C:/Users/jmacdon/Desktop"
> read.metharray.sheet(dir.does.exist)
[read.metharray.sheet] Found the following CSV files:

ADD REPLYlink written 10 days ago by James W. MacDonald48k

I found the error and corrected it, now its working. Thanks a lot.

ADD REPLYlink written 10 days ago by sinha.puja0
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