User: camillab.

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camillab.10
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Posts by camillab.

<prev • 27 results • page 1 of 3 • next >
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Comment: C: PCA and loadings question
... I have no negative loadings at all. Is it normal? the dataset downloaded from NCBI GEO have the normalised reads and not raw counts ...
written 3 days ago by camillab.10
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Comment: C: PCA and loadings question
... So assuming you have a PCA like this : [https://campus.datacamp.com/courses/chip-seq-with-bioconductor-in-r/comparing-chip-seq-samples?ex=2][1] ]you see that the pink samples(=TURP) do not cluster with the purple one (=primary), if I want to see which genes make these samples to not cluster together ...
written 4 days ago by camillab.10
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PCA and loadings question
... Hi! I have a problem with PCA: I don't understand when it's recommended to scale or not and how to identify the loadings for PC1 (so the genes that in theory are most responsible for the variance and so if, I have understood correctly, are responsible to cluster my samples far away on the PC1). I h ...
scale bulkrna loadings pca written 4 days ago by camillab.10
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Comment: C: pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function
... I have tried removing the character columns and it still did not work. but this morning I thought that maybe there were rows = 0 that once scaled give rise to NA and removing them with the following code, works: mouse <-filter_if(Mousebaseline, is.numeric, all_vars((.) != 0)) #remove all row ...
written 12 days ago by camillab.10
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Comment: C: pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function
... yes but why `mouse <- Mousebaseline %>% drop_na()` doesn't work? ...
written 12 days ago by camillab.10
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Comment: C: pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function
... no inf values: . FALSE 205668 ...
written 12 days ago by camillab.10
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Comment: C: pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function
... no the values are RPKMs ...
written 12 days ago by camillab.10
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Comment: C: pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function
... hi! thank you. is this means that there are NAs? if yes, why my code doesn't get rid of them? is.na(mouseUT) %>% table() FALSE TRUE 168102 37566 dim(mouseUT) [1] 6 34278 ...
written 12 days ago by camillab.10
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pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function call (arg 10)
... Hi! I am trying to do an heatmap with pheatmap package but I keep getting this error : > Error in hclust(d, method = method) : NA/NaN/Inf in foreign function > call (arg 10) I have tried with `na.omit()` and looking at the dataset there is not NA. here my dataset: # A tibble: 5 x 8 ...
R pheatmap rna-seq arg10 written 12 days ago by camillab.10
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reactomePA NO plot but I have the results excel file
... Hi, I am trying to perform GO analysis with reacotmePA package and I wanted to see the GO terms for both up (log2FC>1) and down regulated genes (log2Fc<= -1). I am able to get results for the downregulated genes but not for the upregulated genes (FC >2) and I don't understand why since in ...
R reactomepa rna-seq written 22 days ago by camillab.10

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