I have problem with “getGEO” part of this tutorial and i get “.rowNamesDF” error : kasperdanielhansen.github.io/genbioconductor/html/minfi.html
>geoMat <- getGEO("GSE174818")
Found 1 file(s)
GSE174818_series_matrix.txt.gz
Using locally cached version: C:UsersMahyaAppDataLocalTempRtmpsz3t0D/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:UsersMahyaAppDataLocalTempRtmpsz3t0D/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
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