***  MH aa dmso len with replicates 3  ***
LOGFILES
Running METAP SERVER
Wed Aug 2 22:22:02 CEST 2017
ID=1708022221395341
/home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
/home/metap2/data
+ echo 'we are here'
we are here
+ pwd
/home/metap2/public_html/users/1708022221395341
+ hostname
metap
+ uname -a
Linux metap 4.4.0-65-generic #86-Ubuntu SMP Thu Feb 23 17:49:58 UTC 2017 x86_64 x86_64 x86_64 GNU/Li...
+ echo 'this is the environment'
this is the environment
+ env
RATIOS=n
OUTLIER=n
MISSING=n
DATADIR=/home/metap2/data
SHELL=/bin/sh
JOBID=MH aa dmso len with replicates 3
REFERENCE=n
PATH=/home/metap2/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PWD=/home/metap2/public_html/users/1708022221395341
PRIVAT=0
LANG=en_US.UTF-8
SHLVL=1
HOME=/home/metap2
ID=1708022221395341
DEL_METABS=n
FORMAT=csv
LOGNAME=metap2
EMAIL=unknown
USERID=unknown
DEVELOPT=
_=/usr/bin/env
+ echo 'this is a first R script that works on the input data'
this is a first R script that works on the input data
+ '[' '' = werner ']'
+ '[' '' = karsten ']'
+ '[' '' = gabi ']'
+ '[' '' = elisabeth ']'
+ process_metaP_data.R
RUNNING /home/metap2/exec/process_metaP_data.R
Use of uninitialized value $out0 in substitution (s///) at /home/metap2/exec/readAux.pl line 66.
Use of uninitialized value $out0 in substitution (s///) at /home/metap2/exec/readAux.pl line 67.
Use of uninitialized value in transliteration (tr///) at /home/metap2/exec/readAux.pl line 68.
Use of uninitialized value $out0 in concatenation (.) or string at /home/metap2/exec/readAux.pl line...
Use of uninitialized value $max_length in numeric lt (<) at /home/metap2/exec/readAux.pl line 71.
-rw-rw-r-- 1 metap2 metap2 40477 Aug 2 22:22 .R.Rout
adding: kendall.csv (deflated 45%)
adding: KL_cv.csv (deflated 46%)
adding: PCA_PC1_PC3.map (deflated 80%)
adding: PCAcell.line_PC2_PC3.png (deflated 21%)
adding: summary.csv (deflated 48%)
adding: colsToMark.x.csv (deflated 37%)
adding: phenotypes.csv (deflated 74%)
adding: kendall.pdf (deflated 72%)
adding: data_all.csv (deflated 56%)
adding: PCA_PC1_PC2.png (deflated 21%)
adding: PCAtreatment_PC1_PC2.png (deflated 20%)
adding: PCAtreatment_propOfVar.png (deflated 16%)
adding: cv_average.csv (deflated 51%)
adding: processing_log.txt (deflated 58%)
adding: options (deflated 38%)
adding: PCAtreatment_PC1_PC2.map (deflated 80%)
adding: colsToMark.csv (deflated 18%)
adding: PCAtreatment_PC1_PC3.png (deflated 21%)
adding: phenotypes_numeric.csv (deflated 75%)
adding: PCAcell.line.pdf (deflated 81%)
adding: cv.pdf (deflated 92%)
adding: MD_cv.csv (deflated 45%)
adding: hypothesisTests_separated_for_treatment.pdf (deflated 85%)
adding: PCA_PC1_PC2.map (deflated 80%)
adding: JL_cv.csv (deflated 45%)
adding: PCA:cell.line.pdf (deflated 81%)
adding: PCA_PC2_PC3.map (deflated 80%)
adding: PCAtreatment_PC2_PC3.png (deflated 20%)
adding: hypothesisTests_complete_data.pdf (deflated 86%)
adding: pValuesForAllMetabolites__treatment.csv (deflated 43%)
adding: pValuesForAllMetabolites_cell.line_treatment.csv (deflated 67%)
adding: PCAcell.line_PC1_PC3.map (deflated 80%)
adding: PCAtreatment.pdf (deflated 82%)
adding: bonferroni.csv (deflated 32%)
adding: rowsToMark.csv (deflated 77%)
adding: RL_cv.csv (deflated 46%)
adding: metabNamesMapping.csv (deflated 49%)
adding: PCA.pdf (deflated 81%)
adding: out_params.txt (stored 0%)
adding: input (deflated 55%)
adding: KD_cv.csv (deflated 46%)
adding: data.csv (deflated 55%)
adding: phenotypes.txt (deflated 69%)
adding: DU_cv.csv (deflated 46%)
adding: ML_cv.csv (deflated 46%)
adding: phenotypes_for_QC.csv (deflated 70%)
adding: histograms.pdf (deflated 89%)
adding: PCAcell.line_PC2_PC3.map (deflated 80%)
adding: AD_cv.csv (deflated 45%)
adding: upperOutliers.csv (deflated 43%)
adding: pValuesForAllMetabolites__cell.line.csv (deflated 44%)
adding: barplots/1022149992_sbarplot.map (deflated 74%)
adding: barplots/1022150590_sbarplot.map (deflated 74%)
adding: barplots/Thr_barplot_cell.line.png (deflated 17%)
adding: barplots/Cit_barplot_treatment.png (deflated 18%)
adding: barplots/1022150687_sbarplot.map (deflated 74%)
adding: barplots/1022150464_sbarplot.map (deflated 74%)
adding: barplots/Pro_barplot_cell.line.png (deflated 16%)
adding: barplots/Ala_barplot.map (deflated 80%)
adding: barplots/Val_barplot_cell.line.png (deflated 18%)
adding: barplots/Trp_barplot.map (deflated 80%)
adding: barplots/1022150551_sbarplot.png (deflated 50%)
adding: barplots/1022150668_sbarplot.map (deflated 74%)
adding: barplots/1022149988_sbarplot.png (deflated 48%)
adding: barplots/Val_barplot.map (deflated 80%)
adding: barplots/Pro_barplot_treatment.png (deflated 18%)
adding: barplots/Ile_barplot_treatment.png (deflated 23%)
adding: barplots/Lys_barplot.map (deflated 80%)
adding: barplots/Asn_barplot.map (deflated 80%)
adding: barplots/1022150547_sbarplot.png (deflated 52%)
adding: barplots/Gln_barplot.png (deflated 29%)
adding: barplots/1022150620_sbarplot.png (deflated 51%)
adding: barplots/1022150736_sbarplot.png (deflated 53%)
adding: barplots/1022150071_sbarplot.png (deflated 58%)
adding: barplots/1022150649_sbarplot.map (deflated 74%)
adding: barplots/Ala_barplot.png (deflated 24%)
adding: barplots/Ala_barplot_treatment.png (deflated 19%)
adding: barplots/Trp_barplot_cell.line.png (deflated 16%)
adding: barplots/Arg_barplot_cell.line.png (deflated 18%)
adding: barplots/Phe_barplot_treatment.png (deflated 24%)
adding: barplots/Ser_barplot_cell.line.png (deflated 21%)
adding: barplots/Gly_barplot_cell.line.png (deflated 19%)
adding: barplots/Tyr_barplot_treatment.png (deflated 20%)
adding: barplots/1022150634_sbarplot.png (deflated 51%)
adding: barplots/Asp_barplot_treatment.png (deflated 21%)
adding: barplots/Gly_barplot.map (deflated 80%)
adding: barplots/1022150000_sbarplot.png (deflated 49%)
adding: barplots/1022150717_sbarplot.png (deflated 50%)
adding: barplots/1022149992_sbarplot.png (deflated 49%)
adding: barplots/Met_barplot.png (deflated 23%)
adding: barplots/Thr_barplot.map (deflated 81%)
adding: barplots/1022150532_sbarplot.png (deflated 49%)
adding: barplots/Val_barplot_treatment.png (deflated 24%)
adding: barplots/Thr_barplot_treatment.png (deflated 22%)
adding: barplots/1022150498_sbarplot.png (deflated 50%)
adding: barplots/Met_barplot_cell.line.png (deflated 15%)
adding: barplots/1022150048_sbarplot.map (deflated 74%)
adding: barplots/Gln_barplot_cell.line.png (deflated 17%)
adding: barplots/1022150566_sbarplot.map (deflated 74%)
adding: barplots/1022150483_sbarplot.map (deflated 74%)
adding: barplots/1022150620_sbarplot.map (deflated 74%)
adding: barplots/Asn_barplot_treatment.png (deflated 23%)
adding: barplots/Asn_barplot.png (deflated 26%)
adding: barplots/1022150479_sbarplot.map (deflated 74%)
adding: barplots/Ile_barplot.png (deflated 27%)
adding: barplots/1022150634_sbarplot.map (deflated 74%)
adding: barplots/1022150615_sbarplot.png (deflated 53%)
adding: barplots/Asn_barplot_cell.line.png (deflated 17%)
adding: barplots/1022150551_sbarplot.map (deflated 74%)
adding: barplots/1022150691_sbarplot.map (deflated 74%)
adding: barplots/Lys_barplot_cell.line.png (deflated 20%)
adding: barplots/His_barplot.map (deflated 80%)
adding: barplots/1022150450_sbarplot.png (deflated 52%)
adding: barplots/Cit_barplot_cell.line.png (deflated 15%)
adding: barplots/1022150067_sbarplot.map (deflated 74%)
adding: barplots/1022150532_sbarplot.map (deflated 74%)
adding: barplots/Lys_barplot.png (deflated 29%)
adding: barplots/Orn_barplot.png (deflated 30%)
adding: barplots/1022150445_sbarplot.png (deflated 51%)
adding: barplots/Tyr_barplot.map (deflated 80%)
adding: barplots/Orn_barplot.map (deflated 80%)
adding: barplots/Glu_barplot.png (deflated 24%)
adding: barplots/1022150721_sbarplot.map (deflated 74%)
adding: barplots/1022150509_sbarplot.map (deflated 74%)
adding: barplots/Glu_barplot.map (deflated 80%)
adding: barplots/1022150498_sbarplot.map (deflated 74%)
adding: barplots/1022149973_sbarplot.map (deflated 74%)
adding: barplots/1022150571_sbarplot.png (deflated 52%)
adding: barplots/Tyr_barplot.png (deflated 26%)
adding: barplots/His_barplot_cell.line.png (deflated 18%)
adding: barplots/Ala_barplot_cell.line.png (deflated 16%)
adding: barplots/1022150033_sbarplot.png (deflated 58%)
adding: barplots/Trp_barplot_treatment.png (deflated 20%)
adding: barplots/Pro_barplot.png (deflated 24%)
adding: barplots/1022150513_sbarplot.map (deflated 74%)
adding: barplots/Leu_barplot.map (deflated 81%)
adding: barplots/1022150702_sbarplot.png (deflated 50%)
adding: barplots/Trp_barplot.png (deflated 26%)
adding: barplots/Orn_barplot_cell.line.png (deflated 18%)
adding: barplots/1022150479_sbarplot.png (deflated 50%)
adding: barplots/1022150445_sbarplot.map (deflated 74%)
adding: barplots/1022150736_sbarplot.map (deflated 74%)
adding: barplots/1022150668_sbarplot.png (deflated 52%)
adding: barplots/1022149973_sbarplot.png (deflated 51%)
adding: barplots/1022150672_sbarplot.map (deflated 74%)
adding: barplots/Lys_barplot_treatment.png (deflated 23%)
adding: barplots/Orn_barplot_treatment.png (deflated 23%)
adding: barplots/Gln_barplot.map (deflated 81%)
adding: barplots/Leu_barplot_treatment.png (deflated 22%)
adding: barplots/Arg_barplot_treatment.png (deflated 22%)
adding: barplots/1022150431_sbarplot.png (deflated 50%)
adding: barplots/Gly_barplot.png (deflated 28%)
adding: barplots/1022150052_sbarplot.png (deflated 58%)
adding: barplots/Phe_barplot_cell.line.png (deflated 18%)
adding: barplots/1022150717_sbarplot.map (deflated 74%)
adding: barplots/Cit_barplot.png (deflated 22%)
adding: barplots/1022150585_sbarplot.png (deflated 50%)
adding: barplots/1022150585_sbarplot.map (deflated 74%)
adding: barplots/1022150071_sbarplot.map (deflated 75%)
adding: barplots/1022150431_sbarplot.map (deflated 74%)
adding: barplots/Phe_barplot.map (deflated 81%)
adding: barplots/1022150687_sbarplot.png (deflated 50%)
adding: barplots/Leu_barplot.png (deflated 28%)
adding: barplots/1022150086_sbarplot.map (deflated 75%)
adding: barplots/Val_barplot.png (deflated 32%)
adding: barplots/1022150014_sbarplot.map (deflated 74%)
adding: barplots/Asp_barplot_cell.line.png (deflated 18%)
adding: barplots/1022150483_sbarplot.png (deflated 54%)
adding: barplots/1022150590_sbarplot.png (deflated 51%)
adding: barplots/Met_barplot_treatment.png (deflated 21%)
adding: barplots/1022150649_sbarplot.png (deflated 51%)
adding: barplots/1022150067_sbarplot.png (deflated 57%)
adding: barplots/Gln_barplot_treatment.png (deflated 22%)
adding: barplots/1022150528_sbarplot.png (deflated 52%)
adding: barplots/Leu_barplot_cell.line.png (deflated 16%)
adding: barplots/1022150653_sbarplot.map (deflated 74%)
adding: barplots/1022150653_sbarplot.png (deflated 52%)
adding: barplots/Ile_barplot_cell.line.png (deflated 18%)
adding: barplots/Cit_barplot.map (deflated 80%)
adding: barplots/Arg_barplot.map (deflated 80%)
adding: barplots/Tyr_barplot_cell.line.png (deflated 16%)
adding: barplots/1022150464_sbarplot.png (deflated 50%)
adding: barplots/1022150000_sbarplot.map (deflated 74%)
adding: barplots/1022150426_sbarplot.png (deflated 51%)
adding: barplots/1022150426_sbarplot.map (deflated 74%)
adding: barplots/Arg_barplot.png (deflated 27%)
adding: barplots/1022150513_sbarplot.png (deflated 49%)
adding: barplots/1022150528_sbarplot.map (deflated 74%)
adding: barplots/Glu_barplot_treatment.png (deflated 21%)
adding: barplots/1022150691_sbarplot.png (deflated 51%)
adding: barplots/1022150086_sbarplot.png (deflated 58%)
adding: barplots/1022150566_sbarplot.png (deflated 50%)
adding: barplots/1022150014_sbarplot.png (deflated 48%)
adding: barplots/1022150615_sbarplot.map (deflated 74%)
adding: barplots/Ile_barplot.map (deflated 80%)
adding: barplots/Phe_barplot.png (deflated 26%)
adding: barplots/His_barplot.png (deflated 26%)
adding: barplots/Gly_barplot_treatment.png (deflated 23%)
adding: barplots/1022150052_sbarplot.map (deflated 75%)
adding: barplots/1022149988_sbarplot.map (deflated 74%)
adding: barplots/1022150702_sbarplot.map (deflated 74%)
adding: barplots/Pro_barplot.map (deflated 81%)
adding: barplots/1022150721_sbarplot.png (deflated 53%)
adding: barplots/1022150033_sbarplot.map (deflated 74%)
adding: barplots/1022150509_sbarplot.png (deflated 51%)
adding: barplots/Ser_barplot_treatment.png (deflated 26%)
adding: barplots/Ser_barplot.png (deflated 32%)
adding: barplots/1022150048_sbarplot.png (deflated 54%)
adding: barplots/Met_barplot.map (deflated 81%)
adding: barplots/His_barplot_treatment.png (deflated 21%)
adding: barplots/Asp_barplot.map (deflated 81%)
adding: barplots/Thr_barplot.png (deflated 24%)
adding: barplots/1022150571_sbarplot.map (deflated 74%)
adding: barplots/1022150547_sbarplot.map (deflated 74%)
adding: barplots/Glu_barplot_cell.line.png (deflated 17%)
adding: barplots/1022150672_sbarplot.png (deflated 53%)
adding: barplots/1022150450_sbarplot.map (deflated 73%)
adding: barplots/Ser_barplot.map (deflated 81%)
adding: barplots/Asp_barplot.png (deflated 28%)
adding: data_all_beforeCheck.csv (deflated 56%)
adding: PCA:treatment.pdf (deflated 81%)
adding: lowerOutliers.csv (deflated 49%)
adding: data_beforeCheck.csv (deflated 55%)
adding: JD_cv.csv (deflated 46%)
adding: PCA_PC1_PC3.png (deflated 22%)
adding: phenotypes_nominal.csv (deflated 74%)
adding: pca.rotations.csv (deflated 51%)
adding: hypothesisTests_separated_for_cell.line.pdf (deflated 89%)
adding: PCA_propOfVar.png (deflated 19%)
adding: PCAtreatment_PC2_PC3.map (deflated 80%)
adding: PCAcell.line_PC1_PC2.map (deflated 80%)
adding: aux.txt (stored 0%)
adding: AL_cv.csv (deflated 45%)
adding: PCAtreatment_PC1_PC3.map (deflated 80%)
adding: kendall.png (deflated 77%)
adding: server_log.txt (deflated 84%)
adding: metabolitesForDropping.csv (stored 0%)
adding: PCAcell.line_PC1_PC2.png (deflated 20%)
adding: UL_cv.csv (deflated 46%)
adding: pca.rotations_cell.line.csv (deflated 51%)
adding: pValuesForAllMetabolites_treatment_cell.line.csv (deflated 51%)
adding: PCAcell.line_PC1_PC3.png (deflated 21%)
adding: PCA_PC2_PC3.png (deflated 20%)
adding: PCAcell.line_propOfVar.png (deflated 13%)
adding: pca.rotations_cell.line_treatment.csv (deflated 51%)
adding: phenotypes_beforeCheck.csv (deflated 74%)
adding: RD_cv.csv (deflated 46%)
FINISHED with /home/metap2/exec/process_metaP_data.R
+ echo 'these are the files that are now here:'
these are the files that are now here:
+ ls -ltra
total 2152
-rw-r--r-- 1 www-data www-data 5348 Aug 2 22:21 input.tmp
-rw-r--r-- 1 www-data www-data 5348 Aug 2 22:21 input
-rw-r--r-- 1 www-data www-data 936 Aug 2 22:21 phenotypes.txt.tmp
-rw-r--r-- 1 www-data www-data 936 Aug 2 22:21 phenotypes.txt
-rw-r--r-- 1 www-data www-data 0 Aug 2 22:21 aux.txt
-rw-r--r-- 1 www-data www-data 257 Aug 2 22:21 options
-rwxr-xr-x 1 www-data www-data 603 Aug 2 22:21 metaPjob.cmd
drwxrwxrwx 2314 metap2 metap2 258048 Aug 2 22:22 ..
-rw-rw-r-- 1 metap2 metap2 1 Aug 2 22:22 out_params.txt
-rw-rw-r-- 1 metap2 metap2 5347 Aug 2 22:22 input_4R
-rw-rw-r-- 1 metap2 metap2 200 Aug 2 22:22 metabNamesMapping.csv
-rw-rw-r-- 1 metap2 metap2 5391 Aug 2 22:22 data_beforeCheck.csv
-rw-rw-r-- 1 metap2 metap2 1053 Aug 2 22:22 phenotypes_beforeCheck.csv
-rw-rw-r-- 1 metap2 metap2 5922 Aug 2 22:22 data_all_beforeCheck.csv
-rw-rw-r-- 1 metap2 metap2 646 Aug 2 22:22 AD_cv.csv
-rw-rw-r-- 1 metap2 metap2 638 Aug 2 22:22 AL_cv.csv
-rw-rw-r-- 1 metap2 metap2 644 Aug 2 22:22 DU_cv.csv
-rw-rw-r-- 1 metap2 metap2 644 Aug 2 22:22 JD_cv.csv
-rw-rw-r-- 1 metap2 metap2 644 Aug 2 22:22 JL_cv.csv
-rw-rw-r-- 1 metap2 metap2 643 Aug 2 22:22 KD_cv.csv
-rw-rw-r-- 1 metap2 metap2 647 Aug 2 22:22 KL_cv.csv
-rw-rw-r-- 1 metap2 metap2 637 Aug 2 22:22 MD_cv.csv
-rw-rw-r-- 1 metap2 metap2 638 Aug 2 22:22 ML_cv.csv
-rw-rw-r-- 1 metap2 metap2 641 Aug 2 22:22 RD_cv.csv
-rw-rw-r-- 1 metap2 metap2 640 Aug 2 22:22 RL_cv.csv
-rw-rw-r-- 1 metap2 metap2 637 Aug 2 22:22 UL_cv.csv
-rw-rw-r-- 1 metap2 metap2 70908 Aug 2 22:22 cv.pdf
-rw-rw-r-- 1 metap2 metap2 2 Aug 2 22:22 cv.ok
-rw-rw-r-- 1 metap2 metap2 378 Aug 2 22:22 cv_average.csv
-rw-rw-r-- 1 metap2 metap2 12 Aug 2 22:22 metabolitesForDropping.csv
-rw-rw-r-- 1 metap2 metap2 852 Aug 2 22:22 lowerOutliers.csv
-rw-rw-r-- 1 metap2 metap2 673 Aug 2 22:22 upperOutliers.csv
-rw-rw-r-- 1 metap2 metap2 588 Aug 2 22:22 rowsToMark.csv
-rw-rw-r-- 1 metap2 metap2 187 Aug 2 22:22 colsToMark.x.csv
-rw-rw-r-- 1 metap2 metap2 57 Aug 2 22:22 colsToMark.csv
-rw-rw-r-- 1 metap2 metap2 613 Aug 2 22:22 phenotypes_for_QC.csv
-rw-rw-r-- 1 metap2 metap2 913 Aug 2 22:22 phenotypes.csv
-rw-rw-r-- 1 metap2 metap2 5347 Aug 2 22:22 data.csv
-rw-rw-r-- 1 metap2 metap2 5787 Aug 2 22:22 data_all.csv
-rw-rw-r-- 1 metap2 metap2 663 Aug 2 22:22 phenotypes_numeric.csv
-rw-rw-r-- 1 metap2 metap2 913 Aug 2 22:22 phenotypes_nominal.csv
-rw-rw-r-- 1 metap2 metap2 1828 Aug 2 22:22 summary.csv
-rw-rw-r-- 1 metap2 metap2 192710 Aug 2 22:22 histograms.pdf
drwxrwxrwx 2 www-data www-data 12288 Aug 2 22:22 barplots
-rw-rw-r-- 1 metap2 metap2 635 Aug 2 22:22 pValuesForAllMetabolites__cell.line.csv
-rw-rw-r-- 1 metap2 metap2 579 Aug 2 22:22 pValuesForAllMetabolites__treatment.csv
-rw-rw-r-- 1 metap2 metap2 149885 Aug 2 22:22 hypothesisTests_complete_data.pdf
-rw-rw-r-- 1 metap2 metap2 971 Aug 2 22:22 pValuesForAllMetabolites_cell.line_treatment.c...
-rw-rw-r-- 1 metap2 metap2 299450 Aug 2 22:22 hypothesisTests_separated_for_cell.line.pdf
-rw-rw-r-- 1 metap2 metap2 114 Aug 2 22:22 bonferroni.csv
-rw-rw-r-- 1 metap2 metap2 1037 Aug 2 22:22 pValuesForAllMetabolites_treatment_cell.line.c...
-rw-rw-r-- 1 metap2 metap2 174760 Aug 2 22:22 hypothesisTests_separated_for_treatment.pdf
-rw-rw-r-- 1 metap2 metap2 4593 Aug 2 22:22 PCA_PC1_PC2.map
-rw-rw-r-- 1 metap2 metap2 2159 Aug 2 22:22 PCA_PC1_PC2.png
-rw-rw-r-- 1 metap2 metap2 4583 Aug 2 22:22 PCA_PC1_PC3.map
-rw-rw-r-- 1 metap2 metap2 2143 Aug 2 22:22 PCA_PC1_PC3.png
-rw-rw-r-- 1 metap2 metap2 4579 Aug 2 22:22 PCA_PC2_PC3.map
-rw-rw-r-- 1 metap2 metap2 2125 Aug 2 22:22 PCA_PC2_PC3.png
-rw-rw-r-- 1 metap2 metap2 8586 Aug 2 22:22 pca.rotations.csv
-rw-rw-r-- 1 metap2 metap2 14831 Aug 2 22:22 PCA.pdf
-rw-rw-r-- 1 metap2 metap2 4620 Aug 2 22:22 PCAcell.line_PC1_PC2.map
-rw-rw-r-- 1 metap2 metap2 2148 Aug 2 22:22 PCAcell.line_PC1_PC2.png
-rw-rw-r-- 1 metap2 metap2 4610 Aug 2 22:22 PCAcell.line_PC1_PC3.map
-rw-rw-r-- 1 metap2 metap2 2154 Aug 2 22:22 PCAcell.line_PC1_PC3.png
-rw-rw-r-- 1 metap2 metap2 4606 Aug 2 22:22 PCAcell.line_PC2_PC3.map
-rw-rw-r-- 1 metap2 metap2 2167 Aug 2 22:22 PCAcell.line_PC2_PC3.png
-rw-rw-r-- 1 metap2 metap2 16826 Aug 2 22:22 PCAcell.line.pdf
-rw-rw-r-- 1 metap2 metap2 8551 Aug 2 22:22 pca.rotations_cell.line.csv
-rw-rw-r-- 1 metap2 metap2 15714 Aug 2 22:22 PCA:cell.line.pdf
-rw-rw-r-- 1 metap2 metap2 4620 Aug 2 22:22 PCAtreatment_PC1_PC2.map
-rw-rw-r-- 1 metap2 metap2 2147 Aug 2 22:22 PCAtreatment_PC1_PC2.png
-rw-rw-r-- 1 metap2 metap2 4610 Aug 2 22:22 PCAtreatment_PC1_PC3.map
-rw-rw-r-- 1 metap2 metap2 2124 Aug 2 22:22 PCAtreatment_PC1_PC3.png
-rw-rw-r-- 1 metap2 metap2 4606 Aug 2 22:22 PCAtreatment_PC2_PC3.map
-rw-rw-r-- 1 metap2 metap2 2127 Aug 2 22:22 PCAtreatment_PC2_PC3.png
-rw-rw-r-- 1 metap2 metap2 16894 Aug 2 22:22 PCAtreatment.pdf
-rw-rw-r-- 1 metap2 metap2 15782 Aug 2 22:22 PCA:treatment.pdf
-rw-rw-r-- 1 metap2 metap2 8551 Aug 2 22:22 pca.rotations_cell.line_treatment.csv
-rw-rw-r-- 1 metap2 metap2 5277 Aug 2 22:22 kendall.pdf
-rw-rw-r-- 1 metap2 metap2 922 Aug 2 22:22 kendall.csv
-rw-rw-r-- 1 metap2 metap2 40477 Aug 2 22:22 .R.Rout
-rw-rw-r-- 1 metap2 metap2 3574 Aug 2 22:22 kendall.png
-rw-rw-r-- 1 metap2 metap2 2515 Aug 2 22:22 PCAtreatment_propOfVar.png
-rw-rw-r-- 1 metap2 metap2 3007 Aug 2 22:22 PCAcell.line_propOfVar.png
-rw-rw-r-- 1 metap2 metap2 2172 Aug 2 22:22 PCA_propOfVar.png
-rw-rw-r-- 1 metap2 metap2 1620 Aug 2 22:22 processing_log.txt
-rw-rw-r-- 1 metap2 metap2 14849 Aug 2 22:22 server_log.txt
-rw-rw-r-- 1 metap2 metap2 484468 Aug 2 22:22 download.zip
drwxrwxrwx 3 www-data www-data 4096 Aug 2 22:22 .
+ set -
Finishing METAP SERVER
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OPTION:FORMAT:data format: ' csv '
OPTION:MISSING:treat LOD/out of quant. data as missing: ' n '
OPTION:OUTLIER:drop outliers : ' n '
OPTION:REFERENCE:drop reference samples : ' n '
OPTION:DEL_METABS:drop metabolites with cv > 0.25 : ' n '
OPTION:RATIOS:calculate metabolite ratios : ' n '
AUX:Barplots of each metabolite class have equal y axis: TRUE
Fileformat CSV - deleted lines - win-lin
Read CSV dataset with 22 columns and 42 rows
Data format: csv
EXTRACT: 42 samples and 21 metabolites extracted
PHENOTYPES_UPLOAD:Found 36 matched lines with 3 phenotypes specified
REPLICATES:Found REPLICATES as a phenotype for data quality checks
PHENOTYPES_UPLOAD:Found cell.line treatment as non-data quality phenotypes
BATCHES:No batches
Wrote machted dataset to data_all_beforeCheck.csv
DEL_METAB:Found 3 metabolites with cv above 0.25
Wrote extreme outliers into lowerOutliers.csv
Wrote extreme outliers into upperOutliers.csv
42 samples and 21 metabolites in checked data set
Wrote machted dataset to data_all.csv
Phenotype cell.line is nominal
Phenotype treatment is nominal
Phenotype treatment added to numeric phenotypes also
Wrote summary.csv file
21 Distribution plots generated
Boxplots generated
Boxplots generated
Boxplots and hypothesis tests depending on cell.line
Boxplots generated
Boxplots and hypothesis tests depending on treatment
Boxplots generated
1 phenotypes processed for PCA
Wrote kendall correlation table with 21 rows and 2 columns in kendall.csv
Correlation plot generated
Wrote kendall correlation table with 21 rows and 2 columns in kendall.csv
KEGG Data is provided by the Kanehisa Laboratories
for academic use. Any commercial use of KEGG data requires a license
agreement from Pathway Solutions Inc.
The Helmholtz Zentrum München imprint applies.
This page is maintained by Gabi Kastenmüller and Werner Römisch-Margl.
Last modification: 28 December 2009
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