User: demoraesdiogo2017

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Posts by demoraesdiogo2017

<prev • 26 results • page 1 of 3 • next >
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ANOVA for RNA-seq data?
... Hello I have seem some platforms such as GEPIA offering ANOVA for differential gene expression analysis. However, as far as I'm concerned, ANOVA compares the averages and assumes equal distribution and variance among samples, which, as far I have been lead to assume, is uncommon for any kind of RNA ...
anova rna-seq written 10 days ago by demoraesdiogo201710 • updated 10 days ago by kristoffer.vittingseerup2.9k
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Comment: C: correlating focal CNV values with RNA-seq expression
... Haha I must say even though I know the data I don't feel 100% confident of our decisions yet. Thank you for the paper, I believe we will do a similar box plot on fig 4 of the genes we found. Regarding Pearson, we also tested for log2 transformed values, but now you mention Spearman's test it makes ...
written 24 days ago by demoraesdiogo201710
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Comment: C: correlating focal CNV values with RNA-seq expression
... Pearson correlation, forgot to add ...
written 24 days ago by demoraesdiogo201710
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Comment: C: correlating focal CNV values with RNA-seq expression
... Thank you both for the insightful discussion. Let me get into more details of our pipeline: A lot of samples do have low purity and likely have normal tissue mixed in (the truth about TCGA. a lot of samples but low quality imo). What I did first was a global comparison between groups (discovery s ...
written 24 days ago by demoraesdiogo201710
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correlating focal CNV values with RNA-seq expression
... Hello I would like to use the masked copy number segment from TCGA found on Xena browser and correlate it with gene expression values. Both data sets can be found here https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Liver%20Cancer%20(LIHC)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.e ...
cnv rna-seq written 25 days ago by demoraesdiogo201710 • updated 25 days ago by jared.andrews074.1k
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RNAseq differential expression analysis with only a set of genes
... Hello I have RNAseq data (expected counts) from a large set of patients from GTEx and TCGA. However, I am only interested on analyzing the differential expression of a small set of genes (about 25). Can I download the expected counts values of only these genes and run DE analysis of only this set ( ...
differential expression gene set written 4 months ago by demoraesdiogo201710 • updated 4 months ago by ATpoint26k
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Comment: C: subset function limitation in R
... Hello WouterDeCoster I just used those names as examples to shorten the amount of text to explain my issue. My 50 thousand rows consist of gene names, marking TPMs for the 11 thousand columns, which are tissue samples. These are not the actual names of course, but the solution to the problem would s ...
written 9 months ago by demoraesdiogo201710
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(Closed) subset function limitation in R
... Hello all I have a very large dataset, with 11.000 cols and 50.000 rows. I have a list of about 2.000 names which can be found in the columns. To extract only the columns with those 2000 names, I have used the function subset like this mysubset <- subset(mybigdata, select = c("name1", "na ...
subsetting data written 9 months ago by demoraesdiogo201710
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Comment: C: col as names [solved]
... I ended up using `ex -s -c '1d|x' gene_tpm.txt` because that line was irritating me for a while now thanks everyone, problem solved ...
written 9 months ago by demoraesdiogo201710
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Comment: C: col as names
... ooh I should have known that was a bash line now I feel like a double dumbleass, the Vxs are on the first lines and were added by R in a previous instance. I should have known. ![terminal][1] [1]: https://i.ibb.co/VBdFLvC/terminal.png I think I can remove the first line on linux terminal and t ...
written 9 months ago by demoraesdiogo201710

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Popular Question 8 months ago, created a question with more than 1,000 views. For glmnet package lasso error
Popular Question 8 months ago, created a question with more than 1,000 views. For giving a color to null values on heatmap2
Popular Question 9 months ago, created a question with more than 1,000 views. For glmnet package lasso error

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