User: arronar

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arronar140
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Austria
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Posts by arronar

<prev • 130 results • page 1 of 13 • next >
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Comment: C: Is sampling for training and testing, necessary in random forest algorithms
... I'm keeping the ones with accuracy >65% and then the best one of them. I'm doing CV 50 times because I realized that each time, models have different accuracy. E.g the first could have 34% accuracy while the second 72%. If I don't use CV will the algorithm keep the best one? ...
written 5 weeks ago by arronar140
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Is sampling for training and testing, necessary in random forest algorithms
... Hi. I'm trying to apply, random forest algorithm onto microarray results in order to get a list with the most significant predictors. So far I was executing the following pipeline. buildForest <- function (RF.data, storeDir) { acc = numeric() for(i in 1:50){ ...
microarray importance random forest written 5 weeks ago by arronar140 • updated 5 weeks ago by Jean-Karim Heriche15k
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Comment: C: Why GSVA returns a matrix with fewer gene-sets?
... Oh. my god. row.names are in lowercase while the gene-sets in uppercase. That is the cause of the problem. ...
written 6 weeks ago by arronar140
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Comment: C: Why GSVA returns a matrix with fewer gene-sets?
... `> GSC.C2.msigdb` returns : First 50 (out of 4738) gene set names: [1] "KEGG_GLYCOLYSIS..." "KEGG_CITRATE_CY..." "KEGG_PENTOSE_PH..." "KEGG_PENTOSE_AN..." "KEGG_FRUCTOSE_A..." [6] "KEGG_GALACTOSE_..." "KEGG_ASCORBATE_..." "KEGG_FATTY_ACID..." "KEGG_STEROID_BI..." "KEGG_PRIMARY_BI.. ...
written 6 weeks ago by arronar140
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Comment: C: Why GSVA returns a matrix with fewer gene-sets?
... Did not read anywhere in the manual that it performs such kind of filtering ...
written 6 weeks ago by arronar140
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Comment: C: Why GSVA returns a matrix with fewer gene-sets?
... `loadGSC` is from `piano` package. and `class(GSC.C2.msigdb$gsc)` returns "list" Also I tried to provide it a plain list that created as `KEGG <- GSC.C2.msigdb$gsc[1:186]` which `class(KEGG)` is list and `length(KEGG)` is 186, but still the same results. ...
written 6 weeks ago by arronar140
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Comment: C: Why GSVA returns a matrix with fewer gene-sets?
... I'm not applying any filter ...
written 6 weeks ago by arronar140
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Comment: C: Why GSVA returns a matrix with fewer gene-sets?
... I'm having 72 samples. and I'm getting back 6(pathways)x72(samples) instead of 1866(pathways)x72(samples) Here is the command I'm using `gsva_res <- gsva( data, GSC.C2.msigdb$gsc[1:186], mx.diff=FALSE, verbose=TRUE)` and in the console it returns : >Estimating GSVA scores for 6 gene sets. ...
written 6 weeks ago by arronar140
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Why GSVA returns a matrix with fewer gene-sets?
... Hi. I'm trying to run GSVA, using microarray data and using 186 KEGG gene-sets. While I was waiting the output matrix to be 186(pathways)xsamples , is 6(pathways)xsamples. It returns only enrichment values for only 6 of the provided gene-sets and not for all of them. Is that something expected or a ...
gsva microarray written 6 weeks ago by arronar140
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Intuitive explanation of GSVA analysis
... I'm trying to understand the way the GSVA analysis is working behind the scenes.And I was wondering if there is any way to understand it more intuitively the whole process. So at first according to [paper][1] it starts by evaluating whether a gene i is highly or lowly expressed in sample j in the c ...
gsva understanding microarray written 6 weeks ago by arronar140

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