User: zhaolin20042008

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U of Michigan
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Posts by zhaolin20042008

<prev • 22 results • page 1 of 3 • next >
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DiffBind: Error in heights * sapply(called, function(x) x)
... Hello, Rory, Thank you for suggestions at https://support.bioconductor.org/p/103396/#103545. I still failed run with dba.count, however. Here is what I have done.  1. I have update all the packages. when loading Diffbind 2.6, there is no warnings. 2. Then I run dba.count using  summits=150 with sc ...
diffbind dba.count summits written 4 months ago by zhaolin200420080
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Comment: C: Warnings when update DiffBind and running errors
... [52] stringi_1.1.6            edgeR_3.18.1             zlibbioc_1.24.0          [55] gplots_3.0.1             plyr_1.8.4               grid_3.4.2               [58] blob_1.1.0               ggrepel_0.7.0            gdata_2.18.0             [61] lattice_0.20-35          Biostrings_2.46.0        splin ...
written 4 months ago by zhaolin200420080
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Comment: C: Warnings when update DiffBind and running errors
... loaded via a namespace (and not attached):  [1] Category_2.44.0          bitops_1.0-6             bit64_0.9-7               [4] RColorBrewer_1.1-2       progress_1.1.2           Rgraphviz_2.22.0          [7] tools_3.4.2              backports_1.1.1          R6_2.2.2                 [10] KernSmooth_2 ...
written 4 months ago by zhaolin200420080
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Comment: C: Warnings when update DiffBind and running errors
... > sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/lapack/liblapack.so.3.0 locale:  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C                [ ...
written 4 months ago by zhaolin200420080
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Comment: C: Warnings when update DiffBind and running errors
... Hi, Rory, Thank you for suggestions. I still failed run with summits, however. Here is what I have done.  1. I have update all the packages. when loading Diffbind 2.6, there is no warnings. 2. Then I run dba.count using  summits=150 with score default. the error came out again. How could I fix it? ...
written 4 months ago by zhaolin200420080
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Comment: C: How could I upgrade 191 old packages in my directory?
... Thank you. I will contact the administrator.  ...
written 4 months ago by zhaolin200420080
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Comment: C: How could I upgrade 191 old packages in my directory?
... Hi, Martin,  Thank you for suggestions. But it doesn't work in my case. Could you or others suggest more? Many thanks. Zhaolin > BiocInstaller::biocLite() BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28). installation path not writeable, ...
written 4 months ago by zhaolin200420080
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How could I upgrade 191 old packages in my directory?
... Hello, I just upgraded diffbind to 2.6.1 using bioconductor 3.6 in my directory under SSH secure shell. I got 12 warnings. Here is information : https://support.bioconductor.org/p/103396/#103409 To solve the warnings, I think I should upgrade all the packages using biocLite (), but error showed: B ...
bioclite written 4 months ago by zhaolin200420080 • updated 4 months ago by Martin Morgan ♦♦ 21k
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Warnings when update DiffBind and running errors
... Hello, I have been working with DiffBind for 6 months.  When I updated DiffBind 2.6.1 last week I got some warnings. I don't understand what's wrong. I used  R CMD INSTALL DiffBind_2.6.1.tar.gz. same as I installed DiffBind 2.4.8 Warning messages: 1: no function found corresponding to methods expo ...
diffbind dba.count atac-seq written 4 months ago by zhaolin200420080 • updated 4 months ago by Rory Stark2.4k
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Comment: C: DiffBind: failed to run dba.count in SSH
... Many thanks.  1. I will update DIffBind 2.5.  2. Then I will change aligner bam file at the "bamReds" column. Z Zhang ...
written 11 months ago by zhaolin200420080

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