Hi,
As I was trying to run Rolexa package for Solexa GAII ChIP-Seq data, I encountered an irresolvable problem already in the initial step: loading the intensity data. I used 'readIntensities' function included in the ShortRead package as follows:
path = SolexaPath("/data/091029_HWI-EAS419_0050",
imageAnalysisPath="C1-36_Firecrest1.4.0_02-11-2009_SBSUser")
int = readIntensities(path, pattern="s_1_0001", withVariability = FALSE)
---
Error: Input/Output
'readIntensities' failed to parse files
dirPath: 'C1-36_Firecrest1.4.0_02-11-2009_SBSUser'
pattern: 's_1_0001'
type: 'SolexaIntensity'
error: invalid 'times' argument
---
The path to files is correct, it finds the files:
s_1_0001_int.txt.p.gz
s_1_0001_nse.txt.p.gz
s_1_0001_pos.txt
It should pick the *int.txt.p.gz file. But something goes wrong. Any suggestions to resolve this are appreciated!
---
> sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
[4] LC_COLLATE=en_US LC_MONETARY=C LC_MESSAGES=en_US
[7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rolexa_1.2.0 ShortRead_1.4.0 lattice_0.17-26 BSgenome_1.14.0
[5] Biostrings_2.14.3 IRanges_1.4.4 mclust_3.3.2
loaded via a namespace (and not attached):
[1] Biobase_2.6.0 grid_2.10.0 hwriter_1.1
Kind regards,
Maria Y.
As I was trying to run Rolexa package for Solexa GAII ChIP-Seq data, I encountered an irresolvable problem already in the initial step: loading the intensity data. I used 'readIntensities' function included in the ShortRead package as follows:
path = SolexaPath("/data/091029_HWI-EAS419_0050",
imageAnalysisPath="C1-36_Firecrest1.4.0_02-11-2009_SBSUser")
int = readIntensities(path, pattern="s_1_0001", withVariability = FALSE)
---
Error: Input/Output
'readIntensities' failed to parse files
dirPath: 'C1-36_Firecrest1.4.0_02-11-2009_SBSUser'
pattern: 's_1_0001'
type: 'SolexaIntensity'
error: invalid 'times' argument
---
The path to files is correct, it finds the files:
s_1_0001_int.txt.p.gz
s_1_0001_nse.txt.p.gz
s_1_0001_pos.txt
It should pick the *int.txt.p.gz file. But something goes wrong. Any suggestions to resolve this are appreciated!
---
> sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
[4] LC_COLLATE=en_US LC_MONETARY=C LC_MESSAGES=en_US
[7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rolexa_1.2.0 ShortRead_1.4.0 lattice_0.17-26 BSgenome_1.14.0
[5] Biostrings_2.14.3 IRanges_1.4.4 mclust_3.3.2
loaded via a namespace (and not attached):
[1] Biobase_2.6.0 grid_2.10.0 hwriter_1.1
Kind regards,
Maria Y.
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