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How to perform singscore for a dataset from GEO

can i know the procedure to perform singscore for a microarray dataset(affymetrix) and other signatures (gene-sets) . can anyone help with script in R

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updated by GenoMax GenoMax • written by vikram56j • vikram56j

Yes i followed the manual instruction and perform in R I want to perform singscore for a new dataset and gene-set i am facing problem while performing for a new dataset and gene-set

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written by vikram56j • vikram56j

Please edit your question and add a reproducible example with exact error messages or descriptions of unexpected output. Please be as elaborate as you can with the error description.

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written by Ram Ram 
library(singscore)
> # GSE22377_expr_43_se
> # ?DE_YY1_TARGETS_UP
> # ?DE_YY1_TARGETS_UP
> # Have a look at the object GSE22377_expr_43_set containing gene expression data
> # for 43 samples 
> GSE22377_expr_43_se
Error: object 'GSE22377_expr_43_se' not

I had edited the script and tried performing the program i have placed files in a folder and selected the directory but i am getting error can u suggest the format to input the file

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updated by GenoMax GenoMax • written by vikram56j • vikram56j

The error message you’ve copy pasted here is incomplete. Please fix that and also add the output of sessionInfo(). You can edit your posts instead of adding additional comments when the intention is to correct an error in an existing comment.

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written by Ram Ram

The problem is i am not able to input the dataset and gene-sets means in which file should i give the input. can u please suggest the file format or just give me a example file input for dataset and gene-sets and script. it would be helpful to me thank you i have modified the file format also still i am getting error object not found

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written by vikram56j • vikram56j

Please fix the error message and give us the output of sessionInfo(). You also seem to have a typo: You've typed in GSE22377_expr_43_se instead of GSE22377_expr_43_set.

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written by Ram Ram

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