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sinha.puja
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@sinhapuja-18708
Last seen 5.0 years ago
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" |
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.
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.
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.
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:
I found the error and corrected it, now its working. Thanks a lot.