diff --git a/articles/gemma.R.html b/articles/gemma.R.html index 28771dc1..13cffca3 100644 --- a/articles/gemma.R.html +++ b/articles/gemma.R.html @@ -3967,8 +3967,8 @@

Session info
 sessionInfo()
-
R version 4.4.0 (2024-04-24)
-Platform: x86_64-pc-linux-gnu
+
R version 4.3.3 (2024-02-29)
+Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: Ubuntu 22.04.4 LTS
 
 Matrix products: default
@@ -3976,10 +3976,12 @@ 
Session infoSession infoDifferential expression
 

 
Session info
 

-
## R version 4.4.0 (2024-04-24)
-## Platform: x86_64-pc-linux-gnu
+
## R version 4.3.3 (2024-02-29)
+## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Ubuntu 22.04.4 LTS
 ## 
 ## Matrix products: default
@@ -2090,10 +2090,12 @@ 
Session info## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
 ## 
 ## locale:
-##  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
-##  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
-##  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
-## [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
+##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
+##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
+##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
+##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
+##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
+## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
 ## 
 ## time zone: UTC
 ## tzcode source: system (glibc)
@@ -2103,19 +2105,19 @@ 
Session info## 
 ## other attached packages:
 ## [1] purrr_1.0.2      pheatmap_1.0.12  dplyr_1.1.4      gemma.R_3.1.0   
-## [5] BiocStyle_2.31.0
+## [5] BiocStyle_2.30.0
 ## 
 ## loaded via a namespace (and not attached):
 ##  [1] rappdirs_0.3.3      sass_0.4.9          utf8_1.2.4         
 ##  [4] generics_0.1.3      xml2_1.3.6          stringi_1.8.3      
 ##  [7] digest_0.6.35       magrittr_2.0.3      timechange_0.3.0   
-## [10] evaluate_0.23       grid_4.4.0          RColorBrewer_1.1-3 
+## [10] evaluate_0.23       grid_4.3.3          RColorBrewer_1.1-3 
 ## [13] bookdown_0.39       fastmap_1.1.1       jsonlite_1.8.8     
 ## [16] BiocManager_1.30.22 httr_1.4.7          fansi_1.0.6        
 ## [19] viridisLite_0.4.2   scales_1.3.0        textshaping_0.3.7  
 ## [22] jquerylib_0.1.4     cli_3.6.2           rlang_1.1.3        
 ## [25] bit64_4.0.5         munsell_0.5.1       withr_3.0.0        
-## [28] cachem_1.0.8        yaml_2.3.8          tools_4.4.0        
+## [28] cachem_1.0.8        yaml_2.3.8          tools_4.3.3        
 ## [31] memoise_2.0.1       colorspace_2.1-0    kableExtra_1.4.0   
 ## [34] assertthat_0.2.1    curl_5.2.1          vctrs_0.6.5        
 ## [37] R6_2.5.1            lubridate_1.9.3     lifecycle_1.0.4    
@@ -2127,7 +2129,7 @@ 
Session info## [55] xfun_0.43           tibble_3.2.1        tidyselect_1.2.1   
 ## [58] rstudioapi_0.16.0   knitr_1.46          farver_2.1.1       
 ## [61] htmltools_0.5.8.1   svglite_2.1.3       rmarkdown_2.26     
-## [64] compiler_4.4.0

+## [64] compiler_4.3.3

 

   
 
diff --git a/articles/metadata_files/figure-html/unnamed-chunk-19-1.png b/articles/metadata_files/figure-html/unnamed-chunk-19-1.png
index 90fc5a49..d8a0ad0f 100644
Binary files a/articles/metadata_files/figure-html/unnamed-chunk-19-1.png and b/articles/metadata_files/figure-html/unnamed-chunk-19-1.png differ
diff --git a/articles/metanalysis.html b/articles/metanalysis.html
index f0f27651..ac0b97b2 100644
--- a/articles/metanalysis.html
+++ b/articles/metanalysis.html
@@ -919,8 +919,8 @@ 
Session info
 sessionInfo()

-
R version 4.4.0 (2024-04-24)
-Platform: x86_64-pc-linux-gnu
+
R version 4.3.3 (2024-02-29)
+Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: Ubuntu 22.04.4 LTS
 
 Matrix products: default
@@ -928,10 +928,12 @@ 
Session infoSession infoSession info#> attr(,"call")
 #> [1] "https://gemma.msl.ubc.ca/rest/v2/datasets/GSE2018/expressions/genes/10225%2C2841?keepNonSpecific=false"
 #> attr(,"env")
-#> <environment: 0x5607e78fce10>
+#> <environment: 0x55ddd8e58578>
 

     
   
diff --git a/reference/make_design.html b/reference/make_design.html
index fa9e40c7..24f03e77 100644
--- a/reference/make_design.html
+++ b/reference/make_design.html
@@ -111,7 +111,7 @@ 
Examples

 #> Bipolar disorder patient manic phase, 18    c("block....
 #> Bipolar disorder patient manic phase, 29    c("block....
 #> Bipolar disorder patient euthymic phase, 6  c("disea....
-#> Bipolar disorder patient manic phase, 10    c("block....
+#> Bipolar disorder patient manic phase, 10    c("disea....
 #> Control, 2_DE23                             c("disea....
 #> Bipolar disorder patient euthymic phase, 36 c("disea....
 #> Bipolar disorder patient euthymic phase, 19 c("block....