import of HDF5 file into R

Question

[yueli7]

Hello,

I have GSE183206_aggr_filtered_counts_matrix.h5 file downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE183206.

I try to import of HDF5 file into R.

Thank you in advance for great help!

Best regards,

Yue

> library(Seurat)
> library(rhdf5)
> setwd("~/gse183206_lj")
> seurat_data <- Read10X_h5("GSE183206_aggr_filtered_counts_matrix.h5")
Error in H5File.open(filename, mode, file_create_pl, file_access_pl) :
HDF5-API Errors:
error #000: ../../../src/H5F.c in H5Fopen(): line 509: unable to open file
    class: HDF5
    major: File accessibilty
    minor: Unable to open file

error #001: ../../../src/H5Fint.c in H5F__open(): line 1400: unable to open file
    class: HDF5
    major: File accessibilty
    minor: Unable to open file

error #002: ../../../src/H5Fint.c in H5F_open(): line 1700: unable to read superblock
    class: HDF5
    major: File accessibilty
    minor: Read failed

error #003: ../../../src/H5Fsuper.c in H5F__super_read(): line 623: truncated file: eof = 39621079, sblock->base_addr = 0, stored_eof = 67524013
    class: HDF5
    major: File accessibilty
    minor: File has been truncated

Answer 1

[Michael]

If I believed the error messages, I would assume that the file has been truncated and possibly download it again and check its md5sum before loading.

[yueli7]

Hello Michael,

Thank yo for your suggestion!

I should double check the size of the file. It should 67.5MB, not 37MB.

Thank you again and really appreciate your great help!

Best regards,

Yue