DNA Methylation file read

Question

[navienuk2]

Hi,

I tried to read a DNA Methylation data file using the code below

read.bismark(GSE92486_Differential_Gene_expression_Analysis_results_ALold-vs-ALyoung.txt.gz, sampleNames, rmZeroCov = FALSE, strandCollapse = TRUE, fileType = c("cov", "oldBedGraph", "cytosineReport"), mc.cores = 1, verbose = TRUE)

Error in read.bismark(GSE92486_Differential_Gene_expression_Analysis_results_ALold - : unused arguments (fileType = c("cov", "oldBedGraph", "cytosineReport"), mc.cores = 1)1)

i change the code :

data<-read.bismark(GSE92486_Differential_Gene_expression_Analysis_results_ALold-vs-ALyoung.txt.gz, rmZeroCov = FALSE, strandCollapse = TRUE, verbose = TRUE);

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'anyDuplicated': object 'GSE92486_Differential_Gene_expression_Analysis_results_ALold' not found

?? the file is in same folder ?

Answer 1

[ATpoint]

The name "GSE92486_Differential_Gene_expression_Analysis_results_ALold-vs-ALyoung.txt.gz" already suggests that this is some kind of text file that contains analyzed data. Is this even a file that the function expects, so the output of bismark? As for fileType you must give one argument, not multiple, matching the file type you have. I doubt what you plan to do will work as your file is probably not methylation calls.

Is this the content of the file?

Ensembl ID  baseMean    log2FoldChange(AL old / AL young)   lfcSE   stat    pvalue  padj    Gene Symbol
ENSMUSG00000066154  36064.54212 -2.286625564    0.155530237 -14.70212875    6.25E-49    8.53E-45    Mup3
ENSMUSG00000008845  130.5383827 -2.635688938    0.239071206 -11.02470255    2.90E-28    1.98E-24    Cd163
ENSMUSG00000068086  216.9587305 -2.03288885 0.193720109 -10.49394852    9.21E-26    4.19E-22    Cyp2d9
ENSMUSG00000003477  17704.8711  -0.973694031    0.10395382  -9.366601753    7.49E-21    2.56E-17    Inmt
ENSMUSG00000022747  187.5640402 1.468745287 0.168001366 8.742460369 2.28E-18    6.23E-15    St3gal6
ENSMUSG00000059873  30.98011976 2.556940581 0.313171435 8.164667325 3.22E-16    7.33E-13    Olfr1029
ENSMUSG00000043753  59.10810553 2.028671455 0.254909829 7.958388511 1.74E-15    3.40E-12    Dmrta1
ENSMUSG00000041698  303.3438632 -2.827416822    0.359922276 -7.855631642    3.98E-15    6.79E-12    Slco1a1

Pulled it from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92486, as expected this is not bismark output but output from a differential analysis. You cannot load this into that function. Can you explain what you aim to do? I ask because it seems you are not familiar (no offense, we all got started at some point, nothing wrong with that) with the concepts towards which functions or data types exist and which formats need to be loaded into which package.

[navienuk2]

@ATPoint, Thank you. I used readaffy for reading the affymatrix gene expression data. Then I tried read and get the data for https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92486, I have searched the net and i found bismark for DNA methylation reading ? but it does not work ? you got the foldchange, pvalue ..etc i mean the content of file, unzip the file and they are there? but where is the values of expression ? we just have ID ENSMUSG00000066154?

for reading the data ( raw) i must download the raw data ? which packgae read the raw data ? is it look like raw data in affymatrix ? do we have normalization methods for DNA Methylation ??

[ATpoint]

Yes, for raw data you would need to download the raw data, align them with e.g. bismark and then extract methylation calls. These supplementary files are simply what the authors uploaded, and here they provided the methylation results after differential analysis. Since the data are sequencing and not array you cannot use any affymetrix packages. You should google for a methylation pipelines based on NGS if you really want to start from scratch, but this will be cumbersome if you have no experience with it.