User: lessismore

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lessismore370
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Posts by lessismore

<prev • 125 results • page 1 of 13 • next >
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Comment: C: Computing the K for K-means clustering for a set of genes
... i refer to "expression profiles" when talking about scaling for rows (genes) and thus seeing a preferred trend in the expression across samples(and conditions). Could you define QCd? Thanks a lot for your answer Kevin ...
written 20 days ago by lessismore370
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Comment: C: Computing the K for K-means clustering for a set of genes
... I would like to test - if scaling for 1. normalized counts or 2. log2 values (for the eucliden distance is better the second?) - what difference there would be plotting the heatmap based on euclidean distance or Pearson correlation across the genes? - what difference there would be pl ...
written 20 days ago by lessismore370
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Comment: C: Computing the K for K-means clustering for a set of genes
... Can i ask you why you cluster genes by pearson correlation and samples by Spearman? hr <- hclust(as.dist(1-cor(t(scaledata), method="pearson")), method="complete") # Cluster rows by Pearson correlation. hc <- hclust(as.dist(1-cor(scaledata, method="spearman")), method="complete") # Cl ...
written 20 days ago by lessismore370
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Comment: C: Computing the K for K-means clustering for a set of genes
... Hey Kevin, i assume that going for medoids could be preferable because they are always members of the data set. In my case i want to cluster expressed genes based on few samples (8). The idea is cluster those genes in the best way possible (along with the clustering of my samples). They are about f ...
written 20 days ago by lessismore370
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Comment: C: Computing the K for K-means clustering for a set of genes
... Indeed i was talking about outlier genes. Their effect however can be minimized by scaling, correct? Cant wait to read your document. ...
written 22 days ago by lessismore370
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Comment: C: Computing the K for K-means clustering for a set of genes
... I have a doubt. Literally what does it mean "cut the tree"? 1.You remove info? or your force the info to cluster in this predefined number of clusters? ...
written 22 days ago by lessismore370
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Computing the K for K-means clustering for a set of genes
... Conceptual doubts for computing the K: 1) Is it mandatory to scale the dataset before? If yes, why? 2) Is it recommendable to remove outliers before? If yes, what's the best method to evaluate which outlier to exclude? 3) I have seen that the extimated K coud be used also for hierarchic ...
statisics k-means heatmaps clustering written 22 days ago by lessismore370 • updated 22 days ago by Kevin Blighe7.3k
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Comment: C: compare two text file
... grep -f test1.txt test2.txt | grep "Luciferase reporter assay\|qRT-PCR\|Western blot" ...
written 23 days ago by lessismore370
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Comment: C: compare two text file
... In R test <- merge(1st file , 2nd file, by.x="column_1stfile", by.y="column_2ndfile", all.x=T) ...
written 23 days ago by lessismore370
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workflow question - problems with gene annotation
... Workflow question: Im trying to clone a gene. While amplifying it, i had some problems. I then realized that its gene model changes across genome versions meaning that i have the 5' region in the CDS that displays some indels. I have multiple transcripts in both genome versions and i realized i don ...
rnaseq assembly gene annotation written 24 days ago by lessismore370 • updated 24 days ago by colindaven410

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