Question

Reading 450k data in minfi

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lalchungnungabt17 • 0

@lalchungnungabt17-16075

Last seen 4.0 years ago

Hi, I have downloaded 450k data and want to read in minfi. When i downloaded the file it comes with csv, txt and excel files, but it does not have any idat files.

I have tried to read the csv file in minfi according to the tuitorial. But i get below error. Did anybody have the same problem and knows how to solve this? Thank you in advance!

targets <- read.metharray.sheet("/home/GSE36278/", pattern="sample.csv") ##The csv file had been renamed [read.metharray.sheet] 

Found the following CSV files: [1] "/home/GSE36278/sample.csv" 

Warning messages: 

1: In FUN(X[[i]], ...) : Could not infer array name for file: /home/GSE36278//sample.csv 

2: In FUN(X[[i]], ...) : Could not infer slide name for file: /home/GSE36278//sample.csv

rgSet <- read.metharray.exp(targets=targets)

Error in read.metharray.exp(targets = targets) : 

  Need 'Basename' amongst the column names of 'targets'

450K minfi • 2.4k views

ADD COMMENT • link updated 5.8 years ago by laurenz.holcik • 0 • written 5.8 years ago by lalchungnungabt17 • 0

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I had to create the sample sheet myself today because my data came without it and I realized that in my case the read function did actually not use the Basename column but inferred the filenames by pasting slide + "_" + array together and then + "Red"/"Grn". So without those 2 columns which should be the basenames (withoug _Red/Grn) it did not work.

Example: One of my basenames was 4841860009C so I had to put 4841860009 under $Slide and $C under Array. The filenames were accordingly 4841860009CRed.idat and 4841860009C_Grn.idat

Best wishes

ADD REPLY • link 5.8 years ago laurenz.holcik • 0

score 1 · Answer 1 · 2019-02-25

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Yuan Tian ▴ 290

@yuan-tian-13904

Last seen 7 months ago

United Kingdom

Um...the error shows that the program can not infer slides and array information from your csv file, thus it may can not form correct "Basename" of IDAT file loading.

So maybe you can paste part of your csv file here, I suspect the problem is missing or modified "SentrixID" and "SentrixPosition" in your csv file. They are related to basename finding.

ADD COMMENT • link 5.8 years ago Yuan Tian ▴ 290

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Illumina Inc.
[Heading]
Descriptor File Name BS0010894-AQPcontent.bpm
Assay Format Infinium 2
Date Manufactured 06/11/2008
Loci Count 485553
[Assay]
IlmnID Name AddressAID AlleleAProbeSeq AddressBID AlleleBProbeSeq InfiniumDesignType NextBase ColorChannel ForwardSequence GenomeBuild CHR MAPINFO SourceSeq Chromosome36 Coordinate36 Strand ProbeSNPs ProbeSNPs10 RandomLoci Methyl27Loci UCSCRefGeneName UCSCRefGeneAccession UCSCRefGeneGroup UCSCCpGIslandsName RelationtoUCSCCpGIsland Phantom DMR cg00035864 cg00035864 31729416 AAAACACTAACAATCTTATCCACATAAACCCTTAAATTTATCTCAAATTC II AATCCAAAGATGATGGAGGAGTGCCCGCTCATGATGTGAAGTACCTGCTCAGCTGGAAAC[CG]AATTTGAGATAAATTCAAGGGTCTATGTGGACAAGACTGCTAGTGTCTCTCTCTGGATTG 37 Y 8553009 AGACACTAGCAGTCTTGTCCACATAGACCCTTGAATTTATCTCAAATTCG Y 8613009 F TTTY18 NR001550 TSS1500
cg00050873 cg00050873 32735311 ACAAAAAAACAACACACAACTATAATAATTTTTAAAATAAATAAACCCCA 31717405 ACGAAAAAACAACGCACAACTATAATAATTTTTAAAATAAATAAACCCCG I A Red TATCTCTGTCTGGCGAGGAGGCAACGCACAACTGTGGTGGTTTTTGGAGTGGGTGGACCC[CG]GCCAAGACGGCCTGGGCTGACCAGAGACGGGAGGCAGAAAAAGTGGGCAGGTGGTTGCAG 37 Y 9363356 CGGGGTCCACCCACTCCAAAAACCACCACAGTTGTGCGTTGCCTCCTCGC Y 9973356 R TSPY4;FAM197Y2 NM001164471;NR001553 Body;TSS1500 chrY:9363680-9363943 NShore
cg00061679 cg00061679 28780415 AAAACATTAAAAAACTAATTCACTACTATTTAATTACTTTATTTTCCATC II TCAACAAATGAGAGACATTGAAGAACTAATTCACTACTATTTGGTTACTTTATTTTCCAT[CG]AAGAAAACCTCTTTTTAAAAACTAACACATAAATAAAATGAACGAAGAACAAACTAAACG 37 Y 25314171 CGATGGAAAATAAAGTAACCAAATAGTAGTGAATTAGTTCTTCAATGTCT Y 23723559 R DAZ1;DAZ4;DAZ4 NM004081;NM020420;NM001005375 Body;Body;Body
cg00063477 cg00063477 16712347 TATTCTTCCACACAAAATACTAAACRTATATTTACAAAAATACTTCCATC II CTCCTGTACTTGTTCATTAAATAATGATTCCTTGGATATACCAAGTCTGGATAGCGGATT[CG]ATGGAAGCATTTTTGTAAATATACGTTCAGTATTTTGTGTGGAAGAACACAATCTAGCTG 37 Y 22741795 CGATGGAAGCATTTTTGTAAATATACGTTCAGTATTTTGTGTGGAAGAAC Y 21151183 F rs9341313 rs13447379 EIF1AY NM004681 Body chrY:22737825-22738052 SShelf
cg00121626 cg00121626 19779393 AAAACTAATAAAAATAACTTACAAACCAAATACTATACCCTACAACTCTC II AGGTGAATGAAGAGACTAATGGGAGTGGCTTGCAAGCCAGGTACTGTGCCCTACAACTCT[CG]CGCTGCCACAAAAAGCCAATTAACGAAGCAAACTGTTTTATCTTTTCCTCTCCCCAGAAG 37 Y 21664296 AGACTAATGGGAGTGGCTTGCAAGCCAGGTACTGTGCCCTACAACTCTCG Y 20123684 R BCORL2 NR002923 Body chrY:21664481-21665063 NShore
cg00212031 cg00212031 29674443 CCCAATTAACCACAAAAACTAAACAAATTATACAATCAAAAAAACATACA 38703326 CCCAATTAACCGCAAAAACTAAACAAATTATACGATCGAAAAAACGTACG I T Red CCATTGGCCCGCCCCAGTTGGCCGCAGGGACTGAGCAAGTTATGCGGTCGGGAAGACGTG[CG]TTAAAGGGCTGAAGGGGAGGGACGGAACTGACAGTCTCTGTGACAGCTCTGAGGTGGGAG 37 Y 21239348 CGCACGTCTTCCCGACCGCATAACTTGCTCAGTCCCTGCGGCCAACTGGG Y 19698736 R TTTY14 NR001543 TSS200 chrY:21238448-21240005 Island
cg00213748 cg00213748 30703409 TTTTAACACCTAACACCATTTTAACAATAAAAATTCTACAAAAAAAAACA 36767301 TTTTAACGCCTAACACCGTTTTAACGATAAAAATTCTACAAAAAAAAACG I A Red TCTGTGGGACCATTTTAACGCCTGGCACCGTTTTAACGATGGAGGTTCTGCAGGAGGGGG[CG]ACCTGGGGTAGGAGGCGTGCTAGTGGTGGATGACATTGTGGCAGAGATGGAGGTGGTGGC 37 Y 8148233 CGCCCCCTCCTGCAGAACCTCCATCGTTAAAACGGTGCCAGGCGTTAAAA Y 8208233 R chrY:8147877-8148210 SShore

ADD REPLY • link 5.8 years ago lalchungnungabt17 • 0

score 0 · Answer 2 · 2019-03-05

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laurenz.holcik • 0

@laurenzholcik-20105

Last seen 2.7 years ago

Austria

I had to create the sample sheet myself today because my data came without it and I realized that in my case the read function did actually not use the Basename column but inferred the filenames by pasting slide + "" + array together and then + "Red"/"Grn". So without those 2 columns which should be the basenames (withoug _Red/Grn) it did not work.

Example: One of my basenames was 4841860009C so I had to put 4841860009 under $Slide and $C under Array. The filenames were accordingly 4841860009CRed.idat and 4841860009C_Grn.idat

Best wishes

ADD COMMENT • link 5.8 years ago laurenz.holcik • 0

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Hi,

Thanks for the comment! However, my problem is there is no basenames itself in the first place!

ADD REPLY • link 5.8 years ago lalchungnungabt17 • 0

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The content you posted is the array design, not the actually measurements. You should not have to read this file in.

ADD REPLY • link 5.8 years ago Kasper Daniel Hansen ★ 6.5k