Galaxy |

Changeset 1:796a42e10f77 (2018-06-17)

Previous changeset 0:fc89f8c3b777 (2018-06-17) Next changeset 2:412403eec79c (2018-06-17)

Commit message:
planemo upload

removed:
test_data/PE_abundance_GE_abundance_pearson.html

diff -r fc89f8c3b777 -r 796a42e10f77 test_data/PE_abundance_GE_abundance_pearson.html
--- a/test_data/PE_abundance_GE_abundance_pearson.html Sun Jun 17 04:20:06 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,56 +0,0 @@\n-<html><body>\n-<h1>Association between proteomics and transcriptomics data</h1>\n- <font color=\'blue\'><h3>Input data summary</h3></font> <ul> <li>Abbrebiations used: PE (Proteomics) and GE (Transcriptomics) </li> <li>Input PE data dimension (Row Column): 3597 58 </li> <li>Input GE data dimension (Row Column): 191650 14 </li> <li>Protein ID fetched from column: 7 </li> <li>Transcript ID fetched from column: 1 </li> <li>Protein ID type: ensembl_peptide_id_version </li> <li>Transcript ID type: ensembl_transcript_id_version </li> <li>Protein expression data fetched from column: 13 </li> <li>Transcript expression data fetched from column: 10 </li><li>Total Protein ID mapped: 3582 </li> <li>Total Protein ID unmapped: 15 </li> <li>Total Transcript ID mapped: 3582 </li> <li>Total Transcript ID unmapped: 188068 </li></ul><font color=\'blue\'><h3>Download mapped unmapped data</h3></font> <ul><li>Protein mapped data: <a href=" output_fold/PE_mapped.tsv " target="_blank"> Link</a> </li> <li>Protein unmapped data: <a href=" output_fold/PE_unmapped.tsv " target="_blank"> Link</a> </li> <li>Transcript mapped data: <a href=" output_fold/GE_mapped.tsv " target="_blank"> Link</a> </li> <li>Transcript unmapped data: <a href=" output_fold/GE_unmapped.tsv " target="_blank"> Link</a> </li><li>Protein abundance data: <a href=" output_fold/PE_abundance.tsv " target="_blank"> Link</a> </li> <li>Transcript abundance data: <a href=" output_fold/GE_abundance.tsv " target="_blank"> Link</a> </li></ul><ul> <li>Number of entries in Transcriptome data used for correlation: 3582 </li> <li>Number of entries in Proteome data used for correlation: 3582 </li></ul><font color=\'blue\'><h3>Filtering</h3></font> Checking for NA or Inf or -Inf in either Transcriptome or Proteome data, if found, remove those entry<br> <ul> <li>Number of NA found: 88 </li> <li>Number of Inf or -Inf found: 559 </li></ul><ul><li>Protein excluded data with NA or Inf or -Inf: <a href=" output_fold/PE_excluded_NA_Inf.tsv " target="_blank"> Link</a> </li> <li>Transcript excluded data with NA or Inf or -Inf: <a href=" output_fold/GE_excluded_NA_Inf.tsv " target="_blank"> Link</a> </li></ul><font color=\'blue\'><h3>Filtered data summary</h3></font> Excluding entires with abundance values: NA/Inf/-Inf<br> <ul> <li>Number of entries in Transcriptome data remained: 2949 </li> <li>Number of entries in Proteome data remained: 2949 </li></ul><font color=\'blue\'><h3>Proteome data summary</h3></font>\n- <table class="embedded-table" border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#c3f0d6"><th>Parameter</th><th>Value</th></tr><tr><td> </td><td> Min. :-2.98277 </td></tr>\n-<tr><td> </td><td> 1st Qu.:-0.40393 </td></tr>\n-<tr><td> </td><td> Median :-0.07986 </td></tr>\n-<tr><td> </td><td> Mean : 0.00000 </td></tr>\n-<tr><td> </td><td> 3rd Qu.: 0.26061 </td></tr>\n-<tr><td> </td><td> Max. :15.13211 </td></tr>\n-</table>\n-<font color=\'blue\'><h3>Transcriptome data summary</h3></font>\n- <table class="embedded-table" border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#c3f0d6"><th>Parameter</th><th>Value</th></tr><tr><td> </td><td> Min. :-8.33003 </td></tr>\n-<tr><td> </td><td> 1st Qu.:-0.06755 </td></tr>\n-<tr><td> </td><td> Median : 0.09635 </td></tr>\n-<tr><td> </td><td> Mean : 0.00000 </td></tr>\n-<tr><td> </td><td> 3rd Qu.: 0.18103 </td></tr>\n-<tr><td> </td><td> Max. : 8.50430 </td></tr>\n-</table>\n-<font color=\'blue\'><h3>Distribution of Proteome and Transcripome abundance (Box plot and Density plot)</h3></font>\n- <img src="AbundancePlot.png"><font color=\'blue\'><h3>Scatter plot between Proteome and Transcriptome Abundance</h3></font>\n- <img src="AbundancePlot_scatter.png"><font color=\'blue\'><h3>Correlation with all data</h3></font>\n- <table class="embedded-table" border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#c3f0d6"><th>Parameter</th><th>Method 1</th><th>'..b'3 </td> <td> 0.9756628 </td> <td> 0.001209039 </td></tr><tr> <td> ENSMUSP00000081956.8 </td> <td> 3.674308 </td> <td> ENSMUST00000005607 </td> <td> 1.306612 </td> <td> 0.006223403 </td></tr></table><font color=\'blue\'><h3>Scatter plot between Proteome and Transcriptome Abundance, after removal of outliers/influential observations</h3></font>\n- <img src="AbundancePlot_scatter_without_outliers.png"><font color=\'blue\'><h3>Correlation with removal of outliers / influential observations</h3></font>\n- <p>We removed the influential observations and reestimated the correlation values.</p><table class="embedded-table" border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#c3f0d6"><th>Parameter</th><th>Method 1</th><th>Method 2</th><th>Method 3</th></tr><tr><td>Correlation method used</td><td> Pearson\'s product-moment correlation </td><td> Spearman\'s rank correlation rho </td><td> Kendall\'s rank correlation tau </td></tr> <tr><td>Correlation</td><td> 0.01485058 </td><td> 0.0246989 </td><td> 0.01689519 </td></tr> <tr><td>Pvalue</td><td> 0.4273403 </td><td> 0.1867467 </td><td> 0.1918906 </td></tr></table>\n-<font color=\'blue\'><h3>Heatmap of PE and GE abundance values</h3></font>\n-<img src="PE_GE_heatmap.png"><font color=\'blue\'><h3>Kmean clustering</h3></font>\n-Number of Clusters: 5<br><a href=" output_fold/PE_GE_kmeans_clusterpoints.txt " target="_blank">Download cluster list</a><br><img src="PE_GE_kmeans.png"><font color=\'blue\'><h3>Other regression model fitting</h3></font>\n-<ul>\n-\t<li>MAE:mean absolute error</li>\n-\t<li>MSE: mean squared error</li>\n-\t<li>RMSE:root mean squared error ( sqrt(MSE) )</li>\n-\t<li>MAPE:mean absolute percentage error</li>\n-\t</ul>\n-\t<h4><a href="PE_GE_modelfit.pdf" target="_blank">Comparison of model fits</a></h4><table class="embedded-table" border=1 cellspacing=0 cellpadding=5 style="table-layout:auto; "> <tr bgcolor="#c3f0d6"><th>Model</th><th>MAE</th><th>MSE</th><th>RMSE</th><th>MAPE</th><th>Diagnostics Plot</th></tr><tr><td>Linear regression with all data</td><td> 0.5463329 </td><td> 0.9996481 </td><td> 0.999824 </td><td> 0.9996321 </td><td> <a href="PE_GE_lm.pdf" target="_blank">Link</a> </td></tr> <tr><td>Linear regression with removal of outliers</td><td> 0.5404805 </td><td> 1.006281 </td><td> 1.003136 </td><td> 1.455637 </td><td> <a href="PE_GE_lm_without_outliers.pdf" target="_blank">Link</a> </td></tr> <tr><td>Resistant regression (lqs / least trimmed squares method)</td><td> 0.5407598 </td><td> 1.007932 </td><td> 1.003958 </td><td> 1.537172 </td><td> <a href="PE_GE_lqs.pdf" target="_blank">Link</a> </td></tr> <tr><td>Robust regression (rlm / Huber M-estimator method)</td><td> 0.5404879 </td><td> 1.005054 </td><td> 1.002524 </td><td> 1.411806 </td><td> <a href="PE_GE_rlm.pdf" target="_blank">Link</a> </td></tr> <tr><td>Polynomial regression with degree 2</td><td> 0.546322 </td><td> 0.9996472 </td><td> 0.9998236 </td><td> 0.9993865 </td><td> <a href="PE_GE_poly2.pdf" target="_blank">Link</a> </td></tr> <tr><td>Polynomial regression with degree 3</td><td> 0.5469588 </td><td> 0.9976384 </td><td> 0.9988185 </td><td> 1.043158 </td><td> <a href="PE_GE_poly3.pdf" target="_blank">Link</a> </td></tr> <tr><td>Polynomial regression with degree 4</td><td> 0.5467885 </td><td> 0.9975077 </td><td> 0.9987531 </td><td> 1.041541 </td><td> <a href="PE_GE_poly4.pdf" target="_blank">Link</a> </td></tr> <tr><td>Polynomial regression with degree 5</td><td> 0.5467813 </td><td> 0.9975076 </td><td> 0.998753 </td><td> 1.041209 </td><td> <a href="PE_GE_poly5.pdf" target="_blank">Link</a> </td></tr> <tr><td>Polynomial regression with degree 6</td><td> 0.5465911 </td><td> 0.996652 </td><td> 0.9983246 </td><td> 1.056632 </td><td> <a href="PE_GE_poly6.pdf" target="_blank">Link</a> </td></tr> <tr><td>Generalized additive models</td><td> 0.5463695 </td><td> 0.9976796 </td><td> 0.9988391 </td><td> 1.032766 </td><td> <a href="PE_GE_gam.pdf" target="_blank">Link</a> </td></tr> </table>\n\\ No newline at end of file\n'