User: yueli7

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yueli70
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Posts by yueli7

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Comment: C: no replicates data
... Thank you so much for your great help!   ...
written 17 months ago by yueli70
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no replicates data
... Hello,   I have no replicated human cancer cell data, and trying to use edgeR.   In the user's guide "edgeR: differential expression analysis of digital gene expression data", 2.1.1 What to do if you have no replicates 2. Simply pick a reasonable dispersion value.   What of the bcv value is ...
edger written 17 months ago by yueli70 • updated 17 months ago by Gordon Smyth38k
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Comment: C: Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in des
... Thanks, > colData              group_list treated1fb      treated treated2fb      treated treated3fb      treated untreated1fb  untreated untreated2fb  untreated > dds <- DESeqDataSetFromMatrix(countData = exprSet, colData = colData, design = ~ group_list)   ...
written 17 months ago by yueli70
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Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
... Hello, How can I figure out this? Thanks in advance! > head(huang_group_list)                   x 1    549_repair.bam 2      6_repair.bam 3  6plus_repair.bam 4     14_repair.bam 5 14plus_repair.bam   > colData                                    x X549_repair.bam       549_repair.bam X6_re ...
deseq2 written 17 months ago by yueli70
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Comment: C: trouble in install DESeq2
... Thank you so much!   I have fixed it. make install   administrator@ACB-HuangLab-Ubuntu:~$ R R version 3.5.0 (2018-04-23) -- "Joy in Playing" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)   ...
written 17 months ago by yueli70
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Comment: C: trouble in install DESeq2
... Thank you again! I tried another way.   administrator@ACB-HuangLab-Ubuntu:~$ cd R-3.5.0/bin administrator@ACB-HuangLab-Ubuntu:~/R-3.5.0/bin$ R R version 3.2.5 (2016-04-14) -- "Very, Very Secure Dishes" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (6 ...
written 17 months ago by yueli70
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Comment: C: trouble in install DESeq2
... Thank you so much!   I try to use R-3.5.0, but it is still old version. What can I do!   Thank you in advance!     administrator@ACB-HuangLab-Ubuntu:~$ cd R-3.5.0/ administrator@ACB-HuangLab-Ubuntu:~/R-3.5.0$ R R version 3.2.5 (2016-04-14) -- "Very, Very Secure Dishes" Copyright (C) 2016 Th ...
written 17 months ago by yueli70
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Comment: A: trouble in install DESeq2
... So sorry about that: I write in the wrong place.     Thank you so much!   I try to use R-3.5.0, but it is still old version. What can I do!   Thank you in advance!   administrator@ACB-HuangLab-Ubuntu:~$ cd R-3.5.0/ administrator@ACB-HuangLab-Ubuntu:~/R-3.5.0$ R R version 3.2.5 (2016-04-14 ...
written 17 months ago by yueli70
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trouble in install DESeq2
... Hello,   I have trouble in install the package DESeq2.   Thank you in advance!    /home/administrator/R/x86_64-pc-linux-gnu-library/3.2/mgcv/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/ ...
deseq2 package installation written 17 months ago by yueli70
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Answer: A: install RCurl in R
... Thanks everyone,   Your answers have given me great help!   ...
written 4.2 years ago by yueli70

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Popular Question 4.2 years ago, created a question with more than 1,000 views. For install RCurl in R

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