mwsill / mnp_training Goto Github PK

Hi,
Thank you for offering this great Github resource.
I tried to repeat the analysis in the nature paper. But I met some problem, I hope you could help, please.
The pipeline do not work, as:

1. for CNV analysis, you mentioned that 'Two sets of 50 control samples displaying a balanced copy-number profile from both male and female donors were used for normalization.' The 50 samples' data seems not in the GSE accession. I did not see samples labeled as 'normal'. Could you give out the data? And how to integrated them?

2. for CNV analysis, did you use the batch effect removed 'Mset' or the 'MNPpreprocessIllumina processed Mset' ?

3. I saw four batch by:

levels(factor(anno$material:ch1))
[1] "DNA_FFPE" "DNA_KRYO" "FFPE" "Frozen"

Here, what is DNA_FFPE and what is DNA_KRYO? They seemed not explained in the paper, are they also FFPE? If not, how to remove the batch effect?

Thank you very much!

I try to run the preprocessing.R but throwed a error as below, are thosed files' name changed?

Error in read.metharray(filepath, verbose = TRUE): The following specified files do not exist:GSE90496_RAW/GSM2402866_5684819013_R02C01_Grn.idat, GSE90496_RAW/GSM2402915_6929689168_R06C01_Grn.idat, GSE90496_RAW/GSM2402916_6929689168_R01C02_Grn.idat, GSE90496_RAW/GSM2402917_6164621144_R04C02_Grn.idat, GSE90496_RAW/GSM2402918_6969568004_R01C01_Grn.idat, GSE90496_RAW/GSM2402919_6164621144_R04C01_Grn.idat, GSE90496_RAW/GSM2402920_6164621144_R05C01_Grn.idat, GSE90496_RAW/GSM2402921_6164621144_R02C01_Grn.idat, GSE90496_RAW/GSM2402953_6164621144_R03C02_Grn.idat, GSE90496_RAW/GSM2402954_6164621144_R02C02_Grn.idat, GSE90496_RAW/GSM2402955_6164621144_R06C01_Grn.idat, GSE90496_RAW/GSM2402956_6164621144_R01C02_Grn.idat, GSE90496_RAW/GSM2402957_6969568004_R02C01_Grn.idat, GSE90496_RAW/GSM2402958_6929718017_R01C01_Grn.idat, GSE90496_RAW/GSM2402959_6929718027_R01C01_Grn.idat, GSE90496_RAW/GSM2402960_6929718027_R02C01_Grn.idat, GSE90496_RAW/GSM2402961_6929718026_R05C02_Grn.idat, GSE90496_RAW/GSM2402962_6929718027_R06C01_Grn.idat, GSE90496_RAW/GSM2402963_6929718027_R04C01_Grn.idat, GSE90496_RAW/GSM2402974_6929718026_R06C01_Grn.idat, GSE90496_RAW/GSM2402975_6929718026_R01C02_Grn.idat, GSE90496_RAW/GSM2402977_6929718027_R04C02_Grn.idat, GSE90496_RAW/GSM2403026_6929718049_R06C01_Grn.idat, GSE90496_RAW/GSM2403027_6929718049_R03C01_Grn.idat, GSE90496_RAW/GSM2403063_6229017023_R05C01_Grn.idat, GSE90496_RAW/GSM2403068_6229017022_R02C02_Grn.idat, GSE90496_RAW/GSM2403070_6229017022_R06C02_Grn.idat, GSE90496_RAW/GSM2403072_6247004023_R03C02_Grn.idat, GSE90496_RAW/GSM2403073_6247004023_R04C02_Grn.idat, GSE90496_RAW/GSM2403076_6247004024_R03C01_Grn.idat, GSE90496_RAW/GSM2403463_8622007027_R01C01_Grn.idat, GSE90496_RAW/GSM2403496_8622007061_R03C01_Grn.idat, GSE90496_RAW/GSM2403619_8622007130_R04C01_Grn.idat, GSE90496_RAW/GSM2403719_9007225017_R01C02_Grn.idat, GSE90496_RAW/GSM2403893_9297949147_R02C02_Grn.idat, GSE90496_RAW/GSM2404046_9373550131_R02C02_Grn.idat, GSE90496_RAW/GSM2404097_9376538156_R01C02_Grn.idat, GSE90496_RAW/GSM2404098_9376538156_R02C01_Grn.idat, GSE90496_RAW/GSM2404099_9376538156_R03C01_Grn.idat, GSE90496_RAW/GSM2404100_9376538156_R03C02_Grn.idat, GSE90496_RAW/GSM2404119_9376561062_R05C01_Grn.idat, GSE90496_RAW/GSM2404123_9379086124_R05C01_Grn.idat, GSE90496_RAW/GSM2404124_9379086124_R04C01_Grn.idat, GSE90496_RAW/GSM2404125_9379086129_R06C01_Grn.idat, GSE90496_RAW/GSM2404126_9379086129_R01C02_Grn.idat, GSE90496_RAW/GSM2404127_9379086124_R01C02_Grn.idat, GSE90496_RAW/GSM2404128_9379086124_R02C02_Grn.idat, GSE90496_RAW/GSM2404148_9407201022_R06C01_Grn.idat, GSE90496_RAW/GSM2404149_9407201022_R03C02_Grn.idat, GSE90496_RAW/GSM2404150_9407201022_R06C02_Grn.idat, GSE90496_RAW/GSM2404151_9407201021_R02C02_Grn.idat, GSE90496_RAW/GSM2404152_9407201022_R03C01_Grn.idat, GSE90496_RAW/GSM2404153_9407201022_R04C01_Grn.idat, GSE90496_RAW/GSM2404154_9407201022_R01C02_Grn.idat, GSE90496_RAW/GSM2404155_9407201022_R04C02_Grn.idat, GSE90496_RAW/GSM2404156_9407201021_R02C01_Grn.idat, GSE90496_RAW/GSM2404157_9407201021_R06C01_Grn.idat, GSE90496_RAW/GSM2404158_9407201021_R04C02_Grn.idat, GSE90496_RAW/GSM2404159_9407201022_R01C01_Grn.idat, GSE90496_RAW/GSM2404160_9407201022_R05C01_Grn.idat, GSE90496_RAW/GSM2404161_9407201022_R02C02_Grn.idat, GSE90496_RAW/GSM2404162_9407201022_R05C02_Grn.idat, GSE90496_RAW/GSM2404163_9407201025_R01C01_Grn.idat, GSE90496_RAW/GSM2404164_9407201021_R03C01_Grn.idat, GSE90496_RAW/GSM2404165_9407201021_R01C02_Grn.idat, GSE90496_RAW/GSM2404166_9407201021_R05C02_Grn.idat, GSE90496_RAW/GSM2404167_9407201021_R05C01_Grn.idat, GSE90496_RAW/GSM2404168_9407201022_R02C01_Grn.idat, GSE90496_RAW/GSM2404379_9422493151_R06C02_Grn.idat, GSE90496_RAW/GSM2404483_9444374134_R02C02_Grn.idat, GSE90496_RAW/GSM2404519_9444374147_R03C01_Grn.idat, GSE90496_RAW/GSM2404775_9769100007_R02C02_Grn.idat, GSE90496_RAW/GSM2404776_9769100008_R02C01_Grn.idat, GSE90496_RAW/GSM2404833_9533774082_R01C01_Grn.idat, GSE90496_RAW/GSM2404834_9533774082_R03C01_Grn.idat, GSE90496_RAW/GSM2404835_9533774082_R04C01_Grn.idat, GSE90496_RAW/GSM2404836_9533774082_R05C01_Grn.idat, GSE90496_RAW/GSM2404837_9533774082_R06C01_Grn.idat, GSE90496_RAW/GSM2404838_9533774082_R01C02_Grn.idat, GSE90496_RAW/GSM2404839_9533774082_R04C02_Grn.idat, GSE90496_RAW/GSM2404840_9533774082_R06C02_Grn.idat, GSE90496_RAW/GSM2404841_9533774084_R02C01_Grn.idat, GSE90496_RAW/GSM2404842_9533774084_R03C01_Grn.idat, GSE90496_RAW/GSM2404843_9533774084_R04C01_Grn.idat, GSE90496_RAW/GSM2404844_9533774084_R06C01_Grn.idat, GSE90496_RAW/GSM2404854_9534104010_R06C02_Grn.idat, GSE90496_RAW/GSM2404880_9534104026_R01C01_Grn.idat, GSE90496_RAW/GSM2404881_9534104026_R02C01_Grn.idat, GSE90496_RAW/GSM2404882_9534104026_R05C01_Grn.idat, GSE90496_RAW/GSM2404926_9969477003_R01C01_Grn.idat, GSE90496_RAW/GSM2404927_9969477003_R02C01_Grn.idat, GSE90496_RAW/GSM2405010_9969477043_R06C02_Grn.idat, GSE90496_RAW/GSM2405011_9969477044_R01C01_Grn.idat, GSE90496_RAW/GSM2405012_9969477044_R02C02_Grn.idat, GSE90496_RAW/GSM2405013_9969477044_R03C02_Grn.idat, GSE90496_RAW/GSM2405014_9969477044_R06C01_Grn.idat, GSE90496_RAW/GSM2405015_9969477044_R02C01_Grn.idat, GSE90496_RAW/GSM2405016_9969477044_R04C02_Grn.idat, GSE90496_RAW/GSM2405017_9969477044_R01C02_Grn.idat, GSE90496_RAW/GSM2405043_9969477079_R06C02_Grn.idat, GSE90496_RAW/GSM2405081_9969477098_R04C01_Grn.idat, GSE90496_RAW/GSM2405210_9878820127_R04C01_Grn.idat, GSE90496_RAW/GSM2405211_9878820127_R05C01_Grn.idat, GSE90496_RAW/GSM2405251_9878827227_R04C01_Grn.idat, GSE90496_RAW/GSM2405372_3999834063_R02C02_Grn.idat, GSE90496_RAW/GSM2405438_3999875073_R01C01_Grn.idat, GSE90496_RAW/GSM2405448_3999875052_R05C01_Grn.idat, GSE90496_RAW/GSM2405449_3999875052_R01C02_Grn.idat, GSE90496_RAW/GSM2405450_3999875052_R02C02_Grn.idat, GSE90496_RAW/GSM2405520_3998909027_R02C02_Grn.idat, GSE90496_RAW/GSM2405521_3998909027_R03C02_Grn.idat, GSE90496_RAW/GSM2405522_3998909027_R04C02_Grn.idat
Traceback:

1. read.metharray(filepath, verbose = TRUE)
2. stop("The following specified files do not exist:", paste(noexits,
   . collapse = ", "))

Hi,

Is there any way to download the RF classifier and calibration model used for https://www.molecularneuropathology.org/mnp/ and/or the original Capper et al. 2018 publication, rather than training your own?

Thanks

Hi I am currently trying to establish a local methodology for running samples through the MNP.v114b R package

One thing I am struggling to do is obtain the same Calibrated score for a sample when using the online version and when using the local R package equivalent.

Could you please expand a little bit more on that happens to an IDAT pair when they enter the classifier through the online portal.

• How are the IDAT pair preprocessed
• If they are normalized against a reference, what is that reference and how is it preprocessed
• Is there any additional transformation that is applied.

I have attached an image of the results below for comparison between the website and two internal runs with different parameters.
As you can see, the results are different.