Problem with minfi package
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Entering edit mode
25 days ago
Mahya.RM • 0

I have problem with "getGEO" part of this tutorial and i get ".rowNamesDF" error : http://kasperdanielhansen.github.io/genbioconductor/html/minfi.html

>geoMat <- getGEO("GSE174818")
Found 1 file(s)
GSE174818_series_matrix.txt.gz
Using locally cached version: C:\Users\Mahya\AppData\Local\Temp\Rtmpsz3t0D/GSE174818_series_matrix.txt.gz
Rows: 0 Columns: 129                                             
 0s-- Column specification -------------------------------------------
Delimiter: "\t"
chr (129): ID_REF, GSM5331993, GSM5331994, GSM5331995, GSM53319...

i Use spec() to retrieve the full column specification for this data. i Specify the column types or set show_col_types = FALSE to quiet this message.

File stored at: 
C:\Users\Mahya\AppData\Local\Temp\Rtmpsz3t0D/GPL21145.soft
Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length   

->So i cleaned "GSE174818_series_matrix.txt." and import it as "geomat"

 geomat <- read.delim("GSE174818CleanMatrixSerious.t.txt")
> head(geomat)
                     sampleNames Sample_title     ID_REF     age
1 GSM5332043_204776850064_R03C01     COVID_01 GSM5332043 age: 39
2 GSM5332051_204776850072_R03C01     COVID_02 GSM5332051 age: 63
3 GSM5332067_204788470029_R03C01     COVID_03 GSM5332067 age: 33
4 GSM5332059_204776850097_R03C01     COVID_04 GSM5332059 age: 49
5 GSM5332075_204788470031_R03C01     COVID_05 GSM5332075 age: 49
6 GSM5332083_204776850045_R03C01     COVID_06 GSM5332083 age: 45

->but it is df and i cannot define pD for it . this is another error :

 pData(geomat)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘pData’ for signature ‘"data.frame"’

->even i can not merge my "geomat" with "rgSet" too!

 pd <- merge(pData(rgset), geomat, by= sampleNames)
Error in as.vector(x, mode) : 

cannot coerce type 'closure' to vector of type 'any'

what is my mistake and how can i merge "RGChannelSet" with "data.frame" thank you so much

minfi methylation analysis package DNA • 145 views
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Entering edit mode

I don't work with minfi much but I do maintain python's methylsuite package that will let you download, process, and analyze GEO data sets. Check it out, and you can contact me if you need help or have questions, thanks.

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