User: camillab.

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camillab.40
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Posts by camillab.

<prev • 79 results • page 1 of 8 • next >
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Error in y - mu : non-numeric argument to binary operator - linear regression loop
... Hi! I am trying to perform linear regression for age and sex on a dataset with 6 samples and 16757 genes creating a loop. this is my dataset ( I copied the first columns): 'data.frame': 6 obs. of 16757 variables: $ samples : chr "hu-c_lab13" "hu-c_lab15" "hu-c_lab17" "hu ...
R bulkrnaseq linear regression written 35 minutes ago by camillab.40
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Comment: C: Adjusting for confounding variables in RNA-SEQ Differential Expression Analysis
... How would write the loop of the logistic regression model if instead of "Schizophrenia" (so the treatment condition) you want to see how each gene is affected by age and sex independently from the health status of the patient (and so basically and identify the residual)? ...
written 5 hours ago by camillab.40
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Error on Linear regression bulkRNAseq
... Hi! I am trying to do a linear regression for age and sex of a bulk-RNAseq composed of 6 human samples (3 untreated and 3 treated) with a total number of genes of 21011 genes. I am trying to reproduce this [biostar post][1] and I wanted to identify the residues to see how age and sex impact gene ex ...
R linear residue regression written 1 day ago by camillab.40 • updated 13 hours ago by rpolicastro4.0k
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Comment: C: NO FDR <0.05 in the whole dataset
... ok! thank you! Then I will leave it ...
written 10 days ago by camillab.40
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NO FDR <0.05 in the whole dataset
... Hi ! I am trying to calculate the FDR for the p.values in my bulk-RNAseq dataset (unfiltered, so on 21011 genes total, the dataset is composed by 2 conditions and it has 3 samples/condition) but I am not particularly strong in stats so I am confused in the output (so apologies if the question is "s ...
fdr R qvalue rna-seq written 10 days ago by camillab.40 • updated 10 days ago by rpolicastro4.0k
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Comment: C: p.adjusted p value
... thank you! I will definitely try it! (I have 6 samples in total, 3 per condition)! and hopefully,(when) I will be able to get the FASTQ and I will run the gold standard pipeline with DESeq2 or limma. ...
written 13 days ago by camillab.40
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Comment: C: p.adjusted p value
... I know the approach you described is the gold standard but at the moment I do not have access to the raw data and only to FPKM data (normalized reads). Obviously you/bioinformatic will say that my results are not valid if I do not apply the approach you described and I knowI should get the raw data ...
written 13 days ago by camillab.40
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Comment: C: p.adjusted p value
... thank you very much! I will ! ...
written 14 days ago by camillab.40
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Comment: C: p.adjusted p value
... thank you. I have analysed bulk-RNAseq from human samples identifying 500 interesting genes to follow up but considering the intrinsic variability of the human samples (quality/age and status of donor etc), I want to try to set a more stringent threshold for significance (for example using correcte ...
written 14 days ago by camillab.40
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p.adjusted p value
... Hi! I want to calculate the p.adjusted p-value for all genes in my dataset. I have a total of 3294 genes with p.vlue <= 0.05 but when I try to calculate the adjusted p-value all I get is just 1 for all genes. what am I doing wrong? here me code (shown only for those 3194 genes but it gives me t ...
fdr R rna-seq pvalue written 14 days ago by camillab.40 • updated 14 days ago by ATpoint46k

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