User: arronar
arronar • 140
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Posts by arronar
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... 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
arronar • 140
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... 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){
...
written 5 weeks ago by
arronar • 140
• updated
5 weeks ago by
Jean-Karim Heriche ♦ 15k
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... 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
arronar • 140
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... `> 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
arronar • 140
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140
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... Did not read anywhere in the manual that it performs such kind of filtering ...
written 6 weeks ago by
arronar • 140
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... `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
arronar • 140
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140
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... I'm not applying any filter ...
written 6 weeks ago by
arronar • 140
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140
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... 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
arronar • 140
6
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... 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 ...
written 6 weeks ago by
arronar • 140
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... 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 ...
written 6 weeks ago by
arronar • 140
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