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Analyse Data from GEO with minfi #235

Closed AzlanNI closed 2 years ago

AzlanNI commented 2 years ago

Hello Everyone,

My name ist Azlan and i am quite new to minfi.

I downloaded Data from GEO with the Accession Number: GSE186458

Then i used the following code to analyze the data: 

untar("/Users/azlannisar/Desktop/GSE122126_RAW.tar")
head(list.files("/Users/azlannisar/GSM3455865", pattern = "idat"))
idatFiles <- list.files("/Users/azlannisar/GSM3455865", pattern = "idat.gz$", full = TRUE)
sapply(idatFiles, gunzip, overwrite = TRUE)
rgSet <- read.metharray.exp(base = "/Users/azlannisar/GSM3455865")

So the Problem starts with the last command. It resolves in a lot of Warnings and i dont know how to deal with them 

                               array                          size     
GSM3455765_7990895122_R01C01   "IlluminaHumanMethylation450k" "622399" 
GSM3455766_7990895122_R01C02   "IlluminaHumanMethylation450k" "622399" 
GSM3455767_7990895122_R04C01   "IlluminaHumanMethylation450k" "622399" 
GSM3455768_7990895088_R06C02   "IlluminaHumanMethylation450k" "622399" 
GSM3455769_9721366130_R04C01   "IlluminaHumanMethylation450k" "622399" 
GSM3455770_101032610022_R01C01 "IlluminaHumanMethylation450k" "622399" 
GSM3455771_101032610022_R02C01 "IlluminaHumanMethylation450k" "622399" 
GSM3455772_101032610022_R03C01 "IlluminaHumanMethylation450k" "622399" 
GSM3455773_101032610022_R04C01 "IlluminaHumanMethylation450k" "622399" 
GSM3455774_101032610022_R05C01 "IlluminaHumanMethylation450k" "622399" 
GSM3455775_101032610022_R04C02 "IlluminaHumanMethylation450k" "622399" 
GSM3455776_200526580085_R01C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455777_200526580085_R02C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455778_200526580085_R03C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455779_200526580085_R04C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455780_200526580085_R05C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455781_200526580085_R06C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455782_200526580085_R07C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455783_200526580085_R08C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455784_200526580086_R01C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455785_200526580086_R02C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455786_200687110064_R01C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455787_200687110064_R02C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455788_200687110064_R03C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455789_200687110064_R04C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455790_200687110064_R05C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455791_200687110064_R06C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455792_200687110064_R07C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455793_200687110064_R08C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455794_200687110069_R01C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455795_200687110069_R02C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455796_200687110069_R03C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455797_200687110069_R04C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455798_200687110069_R05C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455799_200687110069_R06C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455800_200687110069_R07C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455801_200687110069_R08C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455802_200687110097_R01C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455803_200687110097_R02C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455804_200687110097_R03C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455805_200687110097_R04C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455806_200687110099_R03C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455807_200687110099_R04C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455808_200687110099_R05C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455809_200687110099_R06C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455810_200687110099_R07C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455811_200687110099_R08C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455812_201004820115_R01C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455813_201004820115_R02C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455814_201004820115_R03C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455815_201004820115_R04C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455816_201004820115_R05C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455817_201004820115_R06C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455818_201004820115_R08C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455819_201004820143_R01C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455820_201004820143_R02C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455821_201004820143_R04C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455822_201004820143_R05C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455823_201004820143_R06C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455824_201004820143_R08C01 "IlluminaHumanMethylationEPIC" "1052641"
GSM3455825_201502810014_R05C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455826_201502810024_R04C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455827_201502810024_R05C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455828_201502810024_R06C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455829_201502810024_R07C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455830_201502810024_R08C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455831_201502810028_R01C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455832_201502810028_R06C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455833_202232290146_R02C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455834_202232290160_R05C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455835_202232290160_R06C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455836_202232290208_R08C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455837_202410280057_R01C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455838_202410280057_R02C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455839_202410280057_R03C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455840_202410280057_R04C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455841_202410280057_R05C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455842_202410280057_R06C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455843_202410280057_R07C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455844_202410280057_R08C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455845_202410280077_R01C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455846_202410280077_R02C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455847_202410280077_R03C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455848_202410280077_R04C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455849_202410280077_R05C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455850_202410280077_R06C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455851_202410280077_R07C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455852_202410280077_R08C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455853_202410280178_R01C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455854_202410280178_R02C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455855_202410280178_R03C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455856_202410280178_R04C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455857_202410280178_R05C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455858_202410280178_R06C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455859_202410280178_R07C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455860_202410280178_R08C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455861_202410280180_R02C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455862_202410280180_R03C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455863_202410280180_R04C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455864_202410280180_R07C01 "IlluminaHumanMethylationEPIC" "1051815"
GSM3455865_202410280180_R08C01 "IlluminaHumanMethylationEPIC" "1051815"

Fehler in read.metharray(basenames = commonFiles, extended = extended,  : 
  [read.metharray] Trying to parse different IDAT files, of different size and type.
Zusätzlich: Es gab 50 oder mehr Warnungen (Anzeige der ersten 50 mit warnings())

The warnings() are the following: 

Warnmeldungen:
1: In readChar(con, nchars = n) : truncating string with embedded nuls
2: In readChar(con, nchars = n) : truncating string with embedded nuls
3: In readChar(con, nchars = n) : truncating string with embedded nuls
4: In readChar(con, nchars = n) : truncating string with embedded nuls
5: In readChar(con, nchars = n) : truncating string with embedded nuls
6: In readChar(con, nchars = n) : truncating string with embedded nuls
7: In readChar(con, nchars = n) : truncating string with embedded nuls
8: In readChar(con, nchars = n) : truncating string with embedded nuls
9: In readChar(con, nchars = n) : truncating string with embedded nuls
10: In readChar(con, nchars = n) : truncating string with embedded nuls
11: In readChar(con, nchars = n) : truncating string with embedded nuls
12: In readChar(con, nchars = n) : truncating string with embedded nuls
13: In readChar(con, nchars = n) : truncating string with embedded nuls
14: In readChar(con, nchars = n) : truncating string with embedded nuls
15: In readChar(con, nchars = n) : truncating string with embedded nuls
16: In readChar(con, nchars = n) : truncating string with embedded nuls
17: In readChar(con, nchars = n) : truncating string with embedded nuls
18: In readChar(con, nchars = n) : truncating string with embedded nuls
19: In readChar(con, nchars = n) : truncating string with embedded nuls
20: In readChar(con, nchars = n) : truncating string with embedded nuls
21: In readChar(con, nchars = n) : truncating string with embedded nuls
22: In readChar(con, nchars = n) : truncating string with embedded nuls
23: In readChar(con, nchars = n) : truncating string with embedded nuls
24: In readChar(con, nchars = n) : truncating string with embedded nuls
25: In readChar(con, nchars = n) : truncating string with embedded nuls
26: In readChar(con, nchars = n) : truncating string with embedded nuls
27: In readChar(con, nchars = n) : truncating string with embedded nuls
28: In readChar(con, nchars = n) : truncating string with embedded nuls
29: In readChar(con, nchars = n) : truncating string with embedded nuls
30: In readChar(con, nchars = n) : truncating string with embedded nuls
31: In readChar(con, nchars = n) : truncating string with embedded nuls
32: In readChar(con, nchars = n) : truncating string with embedded nuls
33: In readChar(con, nchars = n) : truncating string with embedded nuls
34: In readChar(con, nchars = n) : truncating string with embedded nuls
35: In readChar(con, nchars = n) : truncating string with embedded nuls
36: In readChar(con, nchars = n) : truncating string with embedded nuls
37: In readChar(con, nchars = n) : truncating string with embedded nuls
38: In readChar(con, nchars = n) : truncating string with embedded nuls
39: In readChar(con, nchars = n) : truncating string with embedded nuls
40: In readChar(con, nchars = n) : truncating string with embedded nuls
41: In readChar(con, nchars = n) : truncating string with embedded nuls
42: In readChar(con, nchars = n) : truncating string with embedded nuls
43: In readChar(con, nchars = n) : truncating string with embedded nuls
44: In readChar(con, nchars = n) : truncating string with embedded nuls
45: In readChar(con, nchars = n) : truncating string with embedded nuls
46: In readChar(con, nchars = n) : truncating string with embedded nuls
47: In readChar(con, nchars = n) : truncating string with embedded nuls
48: In readChar(con, nchars = n) : truncating string with embedded nuls
49: In readChar(con, nchars = n) : truncating string with embedded nuls
50: In readChar(con, nchars = n) : truncating string with embedded nuls

these are the first 50 warnings. So now i dont know how to continue with the data since wi wanted to use the methylation data for my reference set it would be great if someone could help me out.

Thanks a lot!

Kind regards,

Azlan

PeteHaitch commented 2 years ago

Try reading just one file and see if you can get that to work.

This question is better posted to the Bioconductor support forum (https://support.bioconductor.org/). The GitHub issues page is for bugs in the software. I'm going to close this and ask that you please post any follow-up to the support forum.