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length of 'dimnames' [1686] must match that of 'dims' [3]

Answer from @stupidwolf, @benn, @llrs, converted from comments: The error complains about the 1686 rownames, while you have 1684 features. I think something is wrong with the naming of your rows. This ...
1 vote

Normalization of data with RPkM

It's very unlikely that "a RPKM analysis" is the right answer. Assuming you'd like to do differential expression, using tools like DESeq or EdgeR on the count table are likely to be a better ...
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1 vote

beginner RNA-seq Replicate papers

I like Gierlinksi, et al., Bioinformatics, 2015 for this type of problem. I like this paper because the methods are descriptive and clear, they have lots of figures that you can reproduce along the ...
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0 votes

beginner RNA-seq Replicate papers

Here's https://drive.google.com/file/d/1Lwh6ofxi_bb92mB0HoRrMJObE1MmtcMi/view?usp=sharing It is from the book of Methods of mathematical oncology https://github.com/...
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2 votes
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Different results of spearman correlation between TPM and FPKM

This shouldn't be surprising that you see different correlations between gene expression data when expressed in different units. To see why, let's look at how these units are defined. Let's denote the ...
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1 vote
Accepted

Can I Incorporate svaseq() into GSEA/GSVA analysis?

Use removeBatchEffects from limma. The input counts should be on log scale, so vst and ...
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0 votes

beginner RNA-seq Replicate papers

I am a beginner too. I will try the galaxy (training): https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html
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0 votes

How can I get data of single cell RNA sequence with raw count?

If the authors did not provide the raw counts, and I don't think it is compulsory, unfortunately you will need to download the raw data, align and count.
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How to visualize genome track of gene in specific cell-lines?

Answer from @devon-ryan, converted from comments: You'll need BAM or bigWig files for each of the tracks. If you can't find any you'll have to make them yourself from public fastq files. The fastq ...

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