User: bioyas

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Posts by bioyas

<prev • 14 results • page 1 of 2 • next >
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Comment: C: How to Identify Housekeeping genes from gene expression matrix and normalize the
... Thanks for your comment. I will try to do the PCA. Both data sets are coming from RNA seq experiments and I have several groups(samples) and there are 3 replicates for each sample in first data set and 4 replicates for each sample in 2nd data set. As I said before when I use normalization I get tw ...
written 7 days ago by bioyas0
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Comment: C: How to Identify Housekeeping genes from gene expression matrix and normalize the
... I did not apply the PCA part. What I did is normalization using edger and then using removeBatchEffect() from limma package to remove batch effects. After all of this drawing heatmap and hierarchical clustering still shows that the samples are separated based on experiments which means that I could ...
written 9 days ago by bioyas0
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Comment: C: How to Identify Housekeeping genes from gene expression matrix and normalize the
... Thanks for your reply. The tutorial is really helpful and what they are explaining is what I have already tried. The experiments were done separately and thats one of the reasons that they are not at the same scale. I thought that housekeeping gene normalization might be the answer to my question ...
written 9 days ago by bioyas0
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How to Identify Housekeeping genes from gene expression matrix and normalize the data
... Hi everyone, I have a matrix of expression(counts) derived from 2 RNA experiments. I have combined the two experiments . I would like to normalize the data in away that at the end I have the expressions at the same scale and can do Differentially expression analysis. What I have tried so far is u ...
normalization housekeeping genes limma edger R written 9 days ago by bioyas0
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Comment: C: Differential Expression analysis between single cell RNa seq & bulk RNa seq data
... As you said it does not make sense to do this analysis without modification.. IF we do DE without correcting the number of reads with normalization as the transcription is very low in single cell, everything will be Differentially expressed. So I am trying to find a way to scale the reads so that th ...
written 10 weeks ago by bioyas0
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Differential Expression analysis between single cell RNa seq & bulk RNa seq data
... Hi, I have two read count data sets for several samples in one organism. One has been generated from Bulk Ran seq and the other from single cell Ran seq. I would like to find the genes that are Differentially expressed between 2 experiments. For example I am looking for genes that are DE when comp ...
bulk rna seq sc-rna-sq de analysis rna-seq written 10 weeks ago by bioyas0 • updated 10 weeks ago by swbarnes28.6k
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Comment: C: Can the code of a R package be changed? How?
... Hello, I read this thread and I found it really useful. I am going to modify an r package too. I was wondering how can I recompile it through Rstudio. I have downloaded the source code of package and I have modified it. I am not sure how to source it or recompile it in Rstudio? Thanks for your he ...
written 4 months ago by bioyas0
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Comment: C: DEG analysis between 2 samples using edger
... Thank you Kevin for your respond. I understand that the result may not be reliable I do such analysis. I have seen section 2.11 of edger manual and I understand how to deal with the situation when the whole experiment is with replicates or if the whole experiment is without replicates. I know that ...
written 5 months ago by bioyas0
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DEG analysis between 2 samples using edger
... Hello everyone, I have two samples under 2 different conditions. I would like to use edgeR to do DEG analysis between these 2 samples. I have read the edgeR manual and I know that if we have 2 or more biological replicates in both conditions we can use glmQLFit(). Or if we don't have biological re ...
edger rna-seq biological_replicates written 5 months ago by bioyas0 • updated 5 months ago by Gordon Smyth1.9k
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Comment: C: getting 0 counts using hisat2 and feature_count pipeline
... Thanks! I checked that. The Chromosome names were different. I could get the counts. ...
written 8 months ago by bioyas0

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Popular Question 3 months ago, created a question with more than 1,000 views. For How to get the gene expression matrix from GEO while getGEO returns 0 features?

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