Question: Error with Minfi while using read.metharray.exp() and read.metharray function
0
gravatar for hrishi27n
2.8 years ago by
hrishi27n20
hrishi27n20 wrote:

Hello All,

I am trying to test Minfi on my test IDAT files, these are not from the minfidata. I am stuck at the step of creating the RGChannelSet. The code reads both the green and red IDAT's correctly, the basename generated are also correct but before exiting the read.metharray function the execution is halted with the following error. Could you please help me by letting me know if I am doing something wrong?

 

 

My code: 

library(minfi)

baseDir <-"/home/hal9/methylation/test_idats"

targets=read.metharray.sheet(baseDir)

print (targets$Basename)

RGSet <- read.metharray(targets$Basename,verbose=TRUE)

print(RGSet)

Output: 

[read.metharray.sheet] Found the following CSV files:


[1] "/home/hal9/methylation/test_idats/test.csv"

[1] "/home/hal9/methylation/test_idats/200517420015_R03C01"

[2] "/home/hal9/methylation/test_idats/200517420015_R03C01"

[3] "/home/hal9/methylation/test_idats/200517420102_R06C01"

[4] "/home/hal9/methylation/test_idats/200517420102_R06C01"

[read.metharray] Reading200517420015_R03C01_Grn.idat


[read.metharray] Reading200517420015_R03C01_Grn.idat


[read.metharray] Reading200517420102_R06C01_Grn.idat


[read.metharray] Reading200517420102_R06C01_Grn.idat


[read.metharray] Reading200517420015_R03C01_Red.idat


[read.metharray] Reading200517420015_R03C01_Red.idat


[read.metharray] Reading200517420102_R06C01_Red.idat


[read.metharray] Reading200517420102_R06C01_Red.idat


[read.metharray] Read idat files in 11.44seconds


[read.metharray] Creating data matrices ... 

done in6.185seconds


[read.metharray] Instantiating final object ... 

Error in data.frame(numeric(n), row.names = nms) : 

  duplicate row.names: 200517420015_R03C01, 200517420102_R06C01

Calls: read.metharray ... annotatedDataFrameFrom -> annotatedDataFrameFrom -> data.frame

Execution halted

ls -l  of my test_idat directory:


[hal9@mango test_idats]$ ls -l

total 70014

-rw-rw-r-- 1 hal9 hal9 8095249 Nov  9 11:21 200517420015_R03C01_Grn.idat

-rw-rw-r-- 1 hal9 hal9 8095249 Nov  9 11:21 200517420015_R03C01_Red.idat

-rw-rw-r-- 1 hal9 hal9 8095249 Nov  9 11:21 200517420085_R06C02_Grn.idat

-rw-rw-r-- 1 hal9 hal9 8095249 Nov  9 11:21 200517420085_R06C02_Red.idat

-rw-rw-r-- 1 hal9 hal9 8095278 Nov  9 11:21 200517420102_R06C01_Grn.idat

-rw-rw-r-- 1 hal9 hal9 8095278 Nov  9 11:21 200517420102_R06C01_Red.idat

-rw-rw-r-- 1 hal9 hal9     530 Nov 10 13:53 test.csv

Output for the targets:

[1] "/home/hal9/methylation/test_idats/test.csv"

   Sample_Name Sample_Well Sample_Plate Sample_Group Pool_ID       person  age

1 4.640959e+18        <NA>         <NA>         Good    <NA> 4.640959e+18 54.6

2 4.640959e+18        <NA>         <NA>         Good    <NA> 4.640959e+18 54.6

3 6.658291e+18        <NA>         <NA>         Good    <NA> 6.658291e+18 26.1

4 6.658291e+18        <NA>         <NA>         Good    <NA> 6.658291e+18 26.1

    sex status  Array        Slide

1 FALSE   Good R03C01 200517420015

2 FALSE   Good R03C01 200517420015

3 FALSE   Good R06C01 200517420102

4 FALSE   Good R06C01 200517420102

                                               Basename

1 /home/hal9/methylation/test_idats/200517420015_R03C01

2 /home/hal9/methylation/test_idats/200517420015_R03C01

3 /home/hal9/methylation/test_idats/200517420102_R06C01

4 /home/hal9/methylation/test_idats/200517420102_R06C01

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by hrishi27n20
Answer: Error with Minfi while using read.metharray.exp() and read.metharray function
0
gravatar for Kasper Daniel Hansen
2.8 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
You most likely have duplicate rows in the targets. Could you show us a printout of that? Best, Kasper (Sent from my phone.) > On Nov 10, 2016, at 14:14, hrishi27n [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org > User hrishi27n wrote Question: Error with Minfi while using read.metharray.exp() and read.metharray function : > > Hello All, > > I am trying to test Minfi on my test IDAT files, these are not from the minfidata. I am stuck at the step of creating the RGChannelSet. The code reads both the green and red IDAT's correctly, the basename generated are also correct but before exiting the read.metharray function the execution is halted with the following error. Could you please help me by letting me know if I am doing something wrong? > > My code: > > library(minfi) > > baseDir <-"/home/hal9/methylation/test_idats" > > targets=read.metharray.sheet(baseDir) > > print (targets$Basename) > > RGSet <- read.metharray(targets$Basename,verbose=TRUE) > > print(RGSet) > > Output: > > [read.metharray.sheet] Found the following CSV files: > > > > [1] "/home/hal9/methylation/test_idats/test.csv" > > [1] "/home/hal9/methylation/test_idats/200517420015_R03C01" > > [2] "/home/hal9/methylation/test_idats/200517420015_R03C01" > > [3] "/home/hal9/methylation/test_idats/200517420102_R06C01" > > [4] "/home/hal9/methylation/test_idats/200517420102_R06C01" > > [read.metharray] Reading200517420015_R03C01_Grn.idat > > > > [read.metharray] Reading200517420015_R03C01_Grn.idat > > > > [read.metharray] Reading200517420102_R06C01_Grn.idat > > > > [read.metharray] Reading200517420102_R06C01_Grn.idat > > > > [read.metharray] Reading200517420015_R03C01_Red.idat > > > > [read.metharray] Reading200517420015_R03C01_Red.idat > > > > [read.metharray] Reading200517420102_R06C01_Red.idat > > > > [read.metharray] Reading200517420102_R06C01_Red.idat > > > > [read.metharray] Read idat files in 11.44seconds > > > > [read.metharray] Creating data matrices ... > > done in6.185seconds > > > > [read.metharray] Instantiating final object ... > > Error in data.frame(numeric(n), row.names = nms) : > > duplicate row.names: 200517420015_R03C01, 200517420102_R06C01 > > Calls: read.metharray ... annotatedDataFrameFrom -> annotatedDataFrameFrom -> data.frame > > Execution halted > > ls -l of my test_idat directory: > > > > [hal9@mango test_idats]$ ls -l > > total 70014 > > -rw-rw-r-- 1 hal9 hal9 8095249 Nov 9 11:21 200517420015_R03C01_Grn.idat > > -rw-rw-r-- 1 hal9 hal9 8095249 Nov 9 11:21 200517420015_R03C01_Red.idat > > -rw-rw-r-- 1 hal9 hal9 8095249 Nov 9 11:21 200517420085_R06C02_Grn.idat > > -rw-rw-r-- 1 hal9 hal9 8095249 Nov 9 11:21 200517420085_R06C02_Red.idat > > -rw-rw-r-- 1 hal9 hal9 8095278 Nov 9 11:21 200517420102_R06C01_Grn.idat > > -rw-rw-r-- 1 hal9 hal9 8095278 Nov 9 11:21 200517420102_R06C01_Red.idat > > -rw-rw-r-- 1 hal9 hal9 530 Nov 10 13:53 test.csv > > > > > > Post tags: minfi, illumina450k, methylation > > You may reply via email or visit Error with Minfi while using read.metharray.exp() and read.metharray function
ADD COMMENTlink written 2.8 years ago by Kasper Daniel Hansen6.4k

Added the targets output

ADD REPLYlink written 2.8 years ago by hrishi27n20
each combination of (Array, Slide) should occur only once, because they represent a specific array. There are two files per array (one red and one green) but you should only have 1 row in the targets object. On Thu, Nov 10, 2016 at 3:02 PM, hrishi27n [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User hrishi27n <https: support.bioconductor.org="" u="" 11821=""/> wrote Comment: > Error with Minfi while using read.metharray.exp() and read.metharray > function <https: support.bioconductor.org="" p="" 89302="" #89306="">: > > Added the targets output > > ------------------------------ > > Post tags: minfi, illumina450k, methylation > > You may reply via email or visit https://support.bioconductor. > org/p/89302/#89306 >
ADD REPLYlink written 2.8 years ago by Kasper Daniel Hansen6.4k

Got it. It works now. Thank you Sir. :) 

ADD REPLYlink written 2.8 years ago by hrishi27n20
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