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 ?
@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 ??
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.