data correaltion
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12 weeks ago
roniozagam94 ▴ 10

hello, im willing to search correlation between my gene expression data that i got from deseq2 results and mirna data that i have so ill get a target prediction there are 2 df that i own, each one contains the subject names in the columns and the rows are the genes or the miR. was looking for an R package such as anamiR however it wint sync with my version and i cannot get it on. does anyone hace anything to offer? much appreciation!!

correlation deseq2 prediction R target • 407 views
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Please use a little more care while writing your question, it is hard to grasp what you mean. In principle calculating correlation doesn't need any package, you can simply use the cor function. If you want to use a specific package and it isn't compatible with your R version you simply have to install a compatible R version, there are many options to do that but it shouldn't be a show-stopper.

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FYI the cor.test() function will display a p-value in addition to the correlation coefficient.

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however it will not link the connection between the data in the df's. anamiR will load info from databases online and connect each miR with its targeted gene..

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well unfortunatley after downloading the correct r version for the package - its dependecies are not synched with this version and i got lots of warnings.

  1: In install.packages(...) :
  installation of package ‘tidyselect’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘fontawesome’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘xfun’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘cli’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘rematch2’ had non-zero exit status
6: In install.packages(...) :
  installation of package ‘lifecycle’ had non-zero exit status
7: In install.packages(...) :
  installation of package ‘org.Hs.eg.db’ had non-zero exit status
8: In install.packages(...) :
  installation of package ‘magrittr’ had non-zero exit status
9: In install.packages(...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
10: In install.packages(...) :
  installation of package ‘gplots’ had non-zero exit status
11: In install.packages(...) :
  installation of package ‘hms’ had non-zero exit status
12: In install.packages(...) :
  installation of package ‘forcats’ had non-zero exit status
13: In install.packages(...) :
  installation of package ‘bslib’ had non-zero exit status
14: In install.packages(...) :
  installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status
15: In install.packages(...) :
  installation of package ‘highr’ had non-zero exit status
16: In install.packages(...) :
  installation of package ‘labelled’ had non-zero exit status
17: In install.packages(...) :
  installation of package ‘pillar’ had non-zero exit status
18: In install.packages(...) :
  installation of package ‘scales’ had non-zero exit status
19: In install.packages(...) :
  installation of package ‘shiny’ had non-zero exit status
20: In install.packages(...) :
  installation of package ‘knitr’ had non-zero exit status
21: In install.packages(...) :
  installation of package ‘FDb.InfiniumMethylation.hg19’ had non-zero exit status
22: In install.packages(...) :
  installation of package ‘ggplot2’ had non-zero exit status
23: In install.packages(...) :
  installation of package ‘htmlTable’ had non-zero exit status
24: In install.packages(...) :
  installation of package ‘viridis’ had non-zero exit status
25: In install.packages(...) :
  installation of package ‘styler’ had non-zero exit status
26: In install.packages(...) :
  installation of package ‘questionr’ had non-zero exit status
27: In install.packages(...) :
  installation of package ‘klaR’ had non-zero exit status
28: In install.packages(...) :
  installation of package ‘agricolae’ had non-zero exit status
29: In install.packages(update[instlib == l, "Package"], l,  ... :
                          installation of package ‘xfun’ had non-zero exit status
                        30: In install.packages(update[instlib == l, "Package"], l,  ... :
                                                  installation of package ‘lifecycle’ had non-zero exit status
                                                31: In install.packages(update[instlib == l, "Package"], l,  ... :
                                                                          installation of package ‘magrittr’ had non-zero exit status
                                                                        32: In install.packages(update[instlib == l, "Package"], l,  ... :
                                                                                                  installation of package ‘tidyselect’ had non-zero exit status
                                                                                                33: In install.packages(update[instlib == l, "Package"], l,  ... :
                                                                                                                          installation of package ‘cli’ had non-zero exit status
                                                                                                                        34: In install.packages(update[instlib == l, "Package"], l,  ... :
                                                                                                                                                  installation of package ‘memoise’ had non-zero exit status
                                                                                                                                                35: In install.packages(update[instlib == l, "Package"], l,  ... :
                                                                                                                                                                          installation of package ‘highr’ had non-zero exit status
                                                                                                                                                                        36: In install.packages(update[instlib == l, "Package"], l,  ... :
                                                                                                                                                                                                  installation of package ‘scales’ had non-zero exit status
                                                                                                                                                                                                37: In install.packages(update[instlib == l, "Package"], l,  ... :
                                                                                                                                                                                                                          installation of package ‘pillar’ had non-zero exit status
                                                                                                                                                                                                                        38: In install.packages(update[instlib == l, "Package"], l,  ... :
                                                                                                                                                                                                                                                  installation of package ‘forcats’ had non-zero exit status
                                                                                                                                                                                                                                                39: In install.packages(update[instlib == l, "Package"], l,  ... :
                                                                                                                                                                                                                                                                          installation of package ‘hms’ had non-zero exit status
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