![cellprofiler measureobjectneighbors cellprofiler measureobjectneighbors](https://cellprofiler.org/files/cellprofiler/files/examplecolocalization_orig_1.png)
Median and MAD expression values were calculated using RNA-Seq profiles from a total of 1022 cell lines, comprising data from the Cancer Cell Line Encyclopedia (CCLE Barretina, et al.) and cell lines nominated by the CMap team. MAD( X ) is a median absolute deviation of Xġ.4826 is a constant to rescale the score as if the standard deviation of X instead of MAD was used X = is a vector of expression values for a given gene across n cell lines X i is expression value of a given gene in i-th cell line Scores were calculated using robust z-score formula: Z-scores Within Primary Site: Similar to z-scores,īut the reference population used to compute the median and MAD is all CCLE lines from the same lineage with data for that gene.īaseline expression of this gene in each cell line is represented as a z-score (top numbers). Particular gene is all CCLE lines with data for that gene. The reference population used to compute the median and MAD for a The "robust" z-score is resistant to outliers by using median instead of mean and median absolute deviation (MAD) instead of standard deviation. Z-scores: The number of standard deviations that a gene is above or below the population mean is called its z-score.
![cellprofiler measureobjectneighbors cellprofiler measureobjectneighbors](http://d1zymp9ayga15t.cloudfront.net/images/WOUND-IMG.gif)
Post-normalization, the expression values range between 4 and 15 log 2 units, with 4 indicating thatĪ gene is minimally or not expressed and 15 indicating the maximum readout. Such that the expression values were comparable across cell lines, by minimizing technical variationĪnd equalizing their distributions (for details of the normalization, see LISS and QNORM entries in the Connectopedia glossary). Normalization: RNAseq RPKM values were log 2 transformed using log 2(max(RPKM, eps)). However I'm not sure if this tag is supposed to work and needs fixing, or if I should just be using :master instead.Feature Mapping: Ensembl Ids from the source data were mapped to Entrez Gene Ids using gene annotations from NCBI (downloaded on 0). If :latest is actually a bleeding-edge build, then I probably shouldn't be using it. Inde圎rror: index 442 is out of bounds for axis 1 with size 435 Thu Oct 29 17:10:39 2015: Image # 15177, module MeasureObjectIntensity # 8: 28.77 secĮrror detected during run of module MeasureObjectNeighborsįile "/usr/local/src/CellProfiler/cellprofiler/pipeline.py", line 1830, in run_with_yieldįile "/usr/local/src/CellProfiler/cellprofiler/pipeline.py", line 2078, in run_moduleįile "/usr/local/src/CellProfiler/cellprofiler/modules/measureobjectneighbors.py", line 440, in runĭistance_matrix = np.inf Warning: .SAXParser: Property '' is not recognized.ĬP-JAVA 17:09:59.944 ERROR - ".SlideBook6Reader" is not valid.ĬP-JAVA 17:10:00.684 ERROR - ".SlideBook6Reader" is not valid.Įxception in thread "Thread-0" Īt .ZeissLMSReader.isThisType(ZeissLMSReader.java:76)Ĭaught exception in class .ZeissLMSReader.isThisTypeĬP-JAVA 17:10:03.010 ERROR - ".SlideBook6Reader" is not valid.ĬP-JAVA 17:10:03.869 ERROR - ".SlideBook6Reader" is not valid.ĬP-JAVA 17:10:04.446 ERROR - ".SlideBook6Reader" is not valid. Warning: .SAXParser: Feature '' is not recognized.
![cellprofiler measureobjectneighbors cellprofiler measureobjectneighbors](https://cdn-ak.f.st-hatena.com/images/fotolife/t/t_kahi/20190921/20190921104436.png)
Times reported are CPU times for each module, not wall-clock time
![cellprofiler measureobjectneighbors cellprofiler measureobjectneighbors](https://cellprofiler.org/files/cellprofiler/files/examplecolocalization_masked_1.png)
ImportError: No module named ilastik_main ImportError: No module named įile "/usr/local/src/CellProfiler/cellprofiler/modules/ilastik_pixel_classification.py", line 81, in Please follow the instructions onįile "/usr/local/src/CellProfiler/cellprofiler/modules/classifypixels.py", line 82, in įrom import DataMgr, DataItemImage Ilastik import: failed to import the ilastik. Pipeline saved with CellProfiler version 20140723174500