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how to change a GEO integrated dataset into kallisto files which can be import by R-tximport. #243

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13mhzeng opened this issue Jan 4, 2020 · 0 comments

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@13mhzeng
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13mhzeng commented Jan 4, 2020

freshman maybe always in trouble when he use R to do some analysis. even in the first step, sadly.
one day,he tried to import a GEO dataset, GSE109449,by R package-tximport because the primary data was seq by kallisto.

temp=tximport("E:/Single CEll Sequencing/GSE109449/GSE109449_gene_count.csv",type = "kallisto",txIn = FALSE)
there were some errors occuring so he found some way out in this web site:
http:https://www.bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html.
but he didnt know again how to generate a kallisto file by using GEO gene_count he had downloaded before. finally he come to here and hope that some kind gentleman or lady can give him a hand.

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