Rownames error with ParseGEO

[gszetosg]

Hi,

Thanks for developing the package. Was looking to get data from Series GSE236082 and got this error running ParseGEO:

Warning: Data is of class data.frame. Coercing to dgCMatrix.Error in validObject(.Object) : invalid class “LogMap” object: Rownames must be supplied

Any thoughts or fixes?

[showteeth]

Hi,

Currently, scfetch only supports the CellRanger output packaged in TAR file, such as GSE200257. In the initial development, we didn't consider the situation of the supplementary files in the form like GSE236082.

We will update scfetch as soon as possible.

P.S: I got a different error when downloading, can you show me the codes you used?

GSE236082.seu <- ParseGEO(
  acce = "GSE236082", platform = NULL, supp.idx = 1, down.supp = TRUE, supp.type = "10x",
  out.folder = "/path/to/save"
)

Error in ExtractGEOExpSupp10x(acce = acce, supp.idx = supp.idx, timeout = timeout, : Does not support non-tar file for 10x mode!

YB

[showteeth]

Hi @gszetosg ,

Since you didn't reply, I solved this issue according to the error on my machine:

Error in ExtractGEOExpSupp10x(acce = acce, supp.idx = supp.idx, timeout = timeout, : Does not support non-tar file for 10x mode!

Step 1: reinstall scfetch with devtools::install_github("showteeth/scfetch") Step 2: use the following codes (I have tested):

> GSE236082.seu <- ParseGEO(
  acce = "GSE236082", platform = NULL, down.supp = TRUE, supp.type = "10xSingle",
  out.folder = "/Users/soyabean/Desktop/tmp/scdown/issues"
)
> GSE236082.seu
An object of class Seurat 
78357 features across 19607 samples within 1 assay 
Active assay: RNA (78357 features, 0 variable features)

Let me know if you have any problems.

YB