diff --git a/data_integration/data/target_GSE17951.txt b/data_integration/data/target_GSE17951.txt index 2db8b3e..c30951a 100644 --- a/data_integration/data/target_GSE17951.txt +++ b/data_integration/data/target_GSE17951.txt @@ -1,23 +1,23 @@ Name FileName Target -GSE17951_1 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449150.CEL Tumour -GSE17951_2 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449151.CEL Tumour -GSE17951_3 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449160.CEL Tumour -GSE17951_4 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449176.CEL Tumour -GSE17951_5 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449189.CEL Tumour -GSE17951_6 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449198.CEL Tumour -GSE17951_7 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449227.CEL Tumour -GSE17951_8 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449229.CEL Tumour -GSE17951_9 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449230.CEL Tumour -GSE17951_10 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449249.CEL Normal -GSE17951_11 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449250.CEL Normal -GSE17951_12 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449255.CEL Normal -GSE17951_13 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449257.CEL Normal -GSE17951_14 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449258.CEL Normal -GSE17951_15 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449259.CEL Normal -GSE17951_16 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449267.CEL Normal -GSE17951_17 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449269.CEL Normal -GSE17951_18 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449270.CEL Normal -GSE17951_19 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449286.CEL Normal -GSE17951_20 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449289.CEL Normal -GSE17951_21 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449292.CEL Normal -GSE17951_22 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449293.CEL Normal +GSE17951_1 GSE17951/GSM449150.CEL Tumour +GSE17951_2 GSE17951/GSM449151.CEL Tumour +GSE17951_3 GSE17951/GSM449160.CEL Tumour +GSE17951_4 GSE17951/GSM449176.CEL Tumour +GSE17951_5 GSE17951/GSM449189.CEL Tumour +GSE17951_6 GSE17951/GSM449198.CEL Tumour +GSE17951_7 GSE17951/GSM449227.CEL Tumour +GSE17951_8 GSE17951/GSM449229.CEL Tumour +GSE17951_9 GSE17951/GSM449230.CEL Tumour +GSE17951_10 GSE17951/GSM449249.CEL Normal +GSE17951_11 GSE17951/GSM449250.CEL Normal +GSE17951_12 GSE17951/GSM449255.CEL Normal +GSE17951_13 GSE17951/GSM449257.CEL Normal +GSE17951_14 GSE17951/GSM449258.CEL Normal +GSE17951_15 GSE17951/GSM449259.CEL Normal +GSE17951_16 GSE17951/GSM449267.CEL Normal +GSE17951_17 GSE17951/GSM449269.CEL Normal +GSE17951_18 GSE17951/GSM449270.CEL Normal +GSE17951_19 GSE17951/GSM449286.CEL Normal +GSE17951_20 GSE17951/GSM449289.CEL Normal +GSE17951_21 GSE17951/GSM449292.CEL Normal +GSE17951_22 GSE17951/GSM449293.CEL Normal diff --git a/data_integration/data/target_GSE3325.txt b/data_integration/data/target_GSE3325.txt index a421706..69bc510 100644 --- a/data_integration/data/target_GSE3325.txt +++ b/data_integration/data/target_GSE3325.txt @@ -1,13 +1,13 @@ Name FileName Target -GSE3325_1 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE3325/GSM74875.CEL Normal -GSE3325_2 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE3325/GSM74876.CEL Normal -GSE3325_3 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE3325/GSM74877.CEL Normal -GSE3325_4 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE3325/GSM74879.CEL Normal -GSE3325_5 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE3325/GSM74880.CEL Normal -GSE3325_6 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE3325/GSM74881.CEL Tumour -GSE3325_7 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE3325/GSM74882.CEL Tumour -GSE3325_8 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE3325/GSM74883.CEL Tumour -GSE3325_9 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE3325/GSM74884.CEL Tumour -GSE3325_10 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE3325/GSM74885.CEL Tumour -GSE3325_11 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE3325/GSM74886.CEL Tumour -GSE3325_12 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE3325/GSM74887.CEL Tumour +GSE3325_1 GSE3325/GSM74875.CEL Normal +GSE3325_2 GSE3325/GSM74876.CEL Normal +GSE3325_3 GSE3325/GSM74877.CEL Normal +GSE3325_4 GSE3325/GSM74879.CEL Normal +GSE3325_5 GSE3325/GSM74880.CEL Normal +GSE3325_6 GSE3325/GSM74881.CEL Tumour +GSE3325_7 GSE3325/GSM74882.CEL Tumour +GSE3325_8 GSE3325/GSM74883.CEL Tumour +GSE3325_9 GSE3325/GSM74884.CEL Tumour +GSE3325_10 GSE3325/GSM74885.CEL Tumour +GSE3325_11 GSE3325/GSM74886.CEL Tumour +GSE3325_12 GSE3325/GSM74887.CEL Tumour diff --git a/data_integration/data/target_GSE55945.txt b/data_integration/data/target_GSE55945.txt index a5dc017..0aada8b 100644 --- a/data_integration/data/target_GSE55945.txt +++ b/data_integration/data/target_GSE55945.txt @@ -1 +1 @@ -Name FileName Target GSE55945_1 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348933_011508_HGU133_PLUS_2.0_MS_36D6.CEL Tumour GSE55945_2 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348934_110607_HGU133_PLUS_2.0_MS_36C1.CEL Tumour GSE55945_3 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348935_011508_HGU133_PLUS_2.0_MS_36D7.CEL Tumour GSE55945_4 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348939_092707_HGU133_PLUS_2.0_NUGEN_TEST07.CEL Tumour GSE55945_5 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348940_110607_HGU133_PLUS_2.0_MS_36C8.CEL Tumour GSE55945_6 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348941_110807_HGU133_PLUS_2.0_MS_36A1.CEL Tumour GSE55945_7 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348942_110607_HGU133_PLUS_2.0_MS_36C2.CEL Tumour GSE55945_8 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348944_011508_HGU133_PLUS_2.0_MS_36C9.CEL Tumour GSE55945_9 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348945_092707_HGU133_PLUS_2.0_NUGEN_TEST05.CEL Tumour GSE55945_10 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348946_110607_HGU133_PLUS_2.0_MS_36C6.CEL Normal GSE55945_11 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348947_110607_HGU133_PLUS_2.0_MS_36C7.CEL Normal GSE55945_12 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348949_011508_HGU133_PLUS_2.0_MS_36D3.CEL Normal GSE55945_13 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348950_011508_HGU133_PLUS_2.0_MS_36D4.CEL Normal GSE55945_14 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348951_011508_HGU133_PLUS_2.0_MS_36D5.CEL Normal GSE55945_15 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348952_110807_HGU133_PLUS_2.0_MS_36A4.CEL Normal GSE55945_16 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348953_110807_HGU133_PLUS_2.0_MS_36A5.CEL Normal +Name FileName Target GSE55945_1 GSE55945/GSM1348933_011508_HGU133_PLUS_2.0_MS_36D6.CEL Tumour GSE55945_2 GSE55945/GSM1348934_110607_HGU133_PLUS_2.0_MS_36C1.CEL Tumour GSE55945_3 GSE55945/GSM1348935_011508_HGU133_PLUS_2.0_MS_36D7.CEL Tumour GSE55945_4 GSE55945/GSM1348939_092707_HGU133_PLUS_2.0_NUGEN_TEST07.CEL Tumour GSE55945_5 GSE55945/GSM1348940_110607_HGU133_PLUS_2.0_MS_36C8.CEL Tumour GSE55945_6 GSE55945/GSM1348941_110807_HGU133_PLUS_2.0_MS_36A1.CEL Tumour GSE55945_7 GSE55945/GSM1348942_110607_HGU133_PLUS_2.0_MS_36C2.CEL Tumour GSE55945_8 GSE55945/GSM1348944_011508_HGU133_PLUS_2.0_MS_36C9.CEL Tumour GSE55945_9 GSE55945/GSM1348945_092707_HGU133_PLUS_2.0_NUGEN_TEST05.CEL Tumour GSE55945_10 GSE55945/GSM1348946_110607_HGU133_PLUS_2.0_MS_36C6.CEL Normal GSE55945_11 GSE55945/GSM1348947_110607_HGU133_PLUS_2.0_MS_36C7.CEL Normal GSE55945_12 GSE55945/GSM1348949_011508_HGU133_PLUS_2.0_MS_36D3.CEL Normal GSE55945_13 GSE55945/GSM1348950_011508_HGU133_PLUS_2.0_MS_36D4.CEL Normal GSE55945_14 GSE55945/GSM1348951_011508_HGU133_PLUS_2.0_MS_36D5.CEL Normal GSE55945_15 GSE55945/GSM1348952_110807_HGU133_PLUS_2.0_MS_36A4.CEL Normal GSE55945_16 GSE55945/GSM1348953_110807_HGU133_PLUS_2.0_MS_36A5.CEL Normal \ No newline at end of file diff --git a/data_integration/data/target_all.txt b/data_integration/data/target_all.txt index 71c7ddb..e297309 100644 --- a/data_integration/data/target_all.txt +++ b/data_integration/data/target_all.txt @@ -1,36 +1,51 @@ Name FileName Target Dataset -GSE17951_1 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449150.CEL Tumour GSE17951 -GSE17951_2 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449151.CEL Tumour GSE17951 -GSE17951_3 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449160.CEL Tumour GSE17951 -GSE17951_4 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449176.CEL Tumour GSE17951 -GSE17951_5 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449189.CEL Tumour GSE17951 -GSE17951_6 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449198.CEL Tumour GSE17951 -GSE17951_7 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449227.CEL Tumour GSE17951 -GSE17951_8 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449229.CEL Tumour GSE17951 -GSE17951_9 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449230.CEL Tumour GSE17951 -GSE17951_10 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449249.CEL Normal GSE17951 -GSE17951_11 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449250.CEL Normal GSE17951 -GSE17951_12 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449255.CEL Normal GSE17951 -GSE17951_13 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449257.CEL Normal GSE17951 -GSE17951_14 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449258.CEL Normal GSE17951 -GSE17951_15 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449259.CEL Normal GSE17951 -GSE17951_16 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449267.CEL Normal GSE17951 -GSE17951_17 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449269.CEL Normal GSE17951 -GSE17951_18 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449270.CEL Normal GSE17951 -GSE17951_19 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449286.CEL Normal GSE17951 -GSE17951_20 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449289.CEL Normal GSE17951 -GSE17951_21 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449292.CEL Normal GSE17951 -GSE17951_22 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE17951/GSM449293.CEL Normal GSE17951 -GSE55945_1 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348933_011508_HGU133_PLUS_2.0_MS_36D6.CEL Tumour GSE55945 GSE55945_2 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348934_110607_HGU133_PLUS_2.0_MS_36C1.CEL Tumour GSE55945 GSE55945_3 /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/CEL_files/GSE55945/GSM1348935_011508_HGU133_PLUS_2.0_MS_36D7.CEL Tumour GSE55945 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+GSE55945_6 GSE55945/GSM1348941_110807_HGU133_PLUS_2.0_MS_36A1.CEL Tumour GSE55945 +GSE55945_7 GSE55945/GSM1348942_110607_HGU133_PLUS_2.0_MS_36C2.CEL Tumour GSE55945 +GSE55945_8 GSE55945/GSM1348944_011508_HGU133_PLUS_2.0_MS_36C9.CEL Tumour GSE55945 +GSE55945_9 GSE55945/GSM1348945_092707_HGU133_PLUS_2.0_NUGEN_TEST05.CEL Tumour GSE55945 +GSE55945_10 GSE55945/GSM1348946_110607_HGU133_PLUS_2.0_MS_36C6.CEL Normal GSE55945 +GSE55945_11 GSE55945/GSM1348947_110607_HGU133_PLUS_2.0_MS_36C7.CEL Normal GSE55945 +GSE55945_12 GSE55945/GSM1348949_011508_HGU133_PLUS_2.0_MS_36D3.CEL Normal GSE55945 +GSE55945_13 GSE55945/GSM1348950_011508_HGU133_PLUS_2.0_MS_36D4.CEL Normal GSE55945 +GSE55945_14 GSE55945/GSM1348951_011508_HGU133_PLUS_2.0_MS_36D5.CEL Normal GSE55945 +GSE55945_15 GSE55945/GSM1348952_110807_HGU133_PLUS_2.0_MS_36A4.CEL Normal GSE55945 +GSE55945_16 GSE55945/GSM1348953_110807_HGU133_PLUS_2.0_MS_36A5.CEL Normal GSE55945 +GSE3325_1 GSE3325/GSM74875.CEL Normal GSE3325 +GSE3325_2 GSE3325/GSM74876.CEL Normal GSE3325 +GSE3325_3 GSE3325/GSM74877.CEL Normal GSE3325 +GSE3325_4 GSE3325/GSM74879.CEL Normal GSE3325 +GSE3325_5 GSE3325/GSM74880.CEL Normal GSE3325 +GSE3325_6 GSE3325/GSM74881.CEL Tumour GSE3325 +GSE3325_7 GSE3325/GSM74882.CEL Tumour GSE3325 +GSE3325_8 GSE3325/GSM74883.CEL Tumour GSE3325 +GSE3325_9 GSE3325/GSM74884.CEL Tumour GSE3325 +GSE3325_10 GSE3325/GSM74885.CEL Tumour GSE3325 +GSE3325_11 GSE3325/GSM74886.CEL Tumour GSE3325 +GSE3325_12 GSE3325/GSM74887.CEL Tumour GSE3325 diff --git a/data_integration/scripts/Molecular_data_integration.R b/data_integration/scripts/Molecular_data_integration.R index b030f9d..7453304 100644 --- a/data_integration/scripts/Molecular_data_integration.R +++ b/data_integration/scripts/Molecular_data_integration.R @@ -71,7 +71,7 @@ library(gplots) ##### Source script for coloured dendrogram -source("/Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/scripts/a2R_code.R") +source("a2R_code.R") ################################################################################ @@ -87,13 +87,14 @@ source("/Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_ #=============================================================================== ##### Change working directory to data folder -setwd("/Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data") +setwd("../data") ##### Read annotation file pd <- read.AnnotatedDataFrame(filename = "target_GSE17951.txt" ,header = TRUE, row.name = "Name", sep = "\t") +setwd("CEL_files/") ##### Read CEL files into an Affybatch dat <- ReadAffy(filenames = pd$FileName, sampleNames = sampleNames(pd), phenoData = pd) @@ -104,7 +105,7 @@ dat <- ReadAffy(filenames = pd$FileName, sampleNames = sampleNames(pd), phenoDat ##### Data quality control using arrayQualityMetrics package ##### NOTE: Computationally intense step, may take few minutes to complete -arrayQuality <- arrayQualityMetrics(expressionset = dat, outdir = "/Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/QC/GSE17951", reporttitle = "arrayQualityMetrics report for GSE17951", force = TRUE, do.logtransform = TRUE, intgroup = "Target") +arrayQuality <- arrayQualityMetrics(expressionset = dat, outdir = "../QC/GSE17951", reporttitle = "arrayQualityMetrics report for GSE17951", force = TRUE, do.logtransform = TRUE, intgroup = "Target") ##### Report detected samples to excluded from downstream analysis @@ -129,7 +130,7 @@ dat <- ReadAffy(filenames = pd$FileName, sampleNames = sampleNames(pd), phenoDat ##### Data quality control using arrayQualityMetrics package ##### NOTE: Computationally intense step, may take few minutes to complete -arrayQuality <- arrayQualityMetrics(expressionset = dat, outdir = "/Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/QC/GSE55945", reporttitle = "arrayQualityMetrics report for GSE55945", force = TRUE, do.logtransform = TRUE, intgroup = "Target") +arrayQuality <- arrayQualityMetrics(expressionset = dat, outdir = "../QC/GSE55945", reporttitle = "arrayQualityMetrics report for GSE55945", force = TRUE, do.logtransform = TRUE, intgroup = "Target") ##### Report detected samples to excluded from downstream analysis @@ -154,7 +155,7 @@ dat <- ReadAffy(filenames = pd$FileName, sampleNames = sampleNames(pd), phenoDat ##### Data quality control using arrayQualityMetrics package ##### NOTE: Computationally intense step, may take few minutes to complete -arrayQuality <- arrayQualityMetrics(expressionset = dat, outdir = "/Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/QC/GSE3325", reporttitle = "arrayQualityMetrics report for GSE3325", force = TRUE, do.logtransform = TRUE, intgroup = "Target") +arrayQuality <- arrayQualityMetrics(expressionset = dat, outdir = "../QC/GSE3325", reporttitle = "arrayQualityMetrics report for GSE3325", force = TRUE, do.logtransform = TRUE, intgroup = "Target") ##### Report detected samples to excluded from downstream analysis @@ -204,7 +205,7 @@ QCnuse@outliers ##### Customising arrayQualityMetrics report qm <- list("Boxplot" = QCboxplot, "Heatmap" = QCheatmap, "MAplot" = QCmaplot, "RLE" = QCrle, "NUSE" = QCnuse) -aqm.writereport(modules = qm, reporttitle = "arrayQualityMetrics report for GSE3325", outdir = "/Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/QC/GSE3325_custom", arrayTable = pData(dat)) +aqm.writereport(modules = qm, reporttitle = "arrayQualityMetrics report for GSE3325", outdir = "../QC/GSE3325_custom", arrayTable = pData(dat)) @@ -259,13 +260,12 @@ pd <- pd[setdiff(sampleNames(pd), as.vector(samples2exclude))] dat <- ReadAffy(filenames = pd$FileName, sampleNames = sampleNames(pd), phenoData = pd) - -##### Create folder for results -system("mkdir /Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/results") - ##### Change working directory to results folder -setwd("/Users/marzec01/Desktop/others/workshops/Lechu_Slowacja_bix_workshop_08_2016/workshop/data/results") +setwd("../") +##### Create folder for results +system("mkdir results") +setwd("results/") #===============================================================================