Moderator: seidel

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seidel6.5k
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I work as a scientist at a non-profit research institute.

Posts by seidel

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Comment: C: Affymetrix Soybean Gene 1.1 ST Array PROBES IDs to Ensembl transcripts IDs
... Have you looked at the affymetrix annotation website https://www.affymetrix.com/analysis/index.affx ? They usually have both a database for looking up annotation for any probe set as well as a download section for downloading files of annotated probes (i.e. which gene /transcript ids match which pro ...
written 13 days ago by seidel6.5k
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Comment: C: ORFs extractor tool
... Can you give a little more context/information? You mean it finds ORFs in a sequence with a known error? (i.e. it would have to know the ORF sequence in advance) What are you actually trying to accomplish? ...
written 18 days ago by seidel6.5k
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Comment: C: Comparing work done on RNA seq data
... Your question is far too vague to answer. What is the purpose of your paper? How is what you might be proposing in your paper relevant to the paper you cite? What is the subject of your paper? ...
written 25 days ago by seidel6.5k
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Comment: C: What is the meaning of the level in groupGO Clusterprofiler ?
... See the answer to [Question: levels in gene ontology][1] ([https://www.biostars.org/p/237816/#237840][2]) [1]: https://www.biostars.org/p/237816/ [2]: https://www.biostars.org/p/237816/#237840 ...
written 28 days ago by seidel6.5k
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Comment: C: single cell RNAseq: From counts or RPKM > PCA > tSNE visualization of PCA
... @noorpratap.singh is telling you to walk through the Seurat tutorial, as it is a good instructional reference/discussion using R on the things you would like to do. ...
written 28 days ago by seidel6.5k
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Answer: A: What is the difference between gene FPKM and transcript FPKM values?
... It depends on what software you're using, and what you are actually quantifying. Most people gloss over the issue because transcripts and genes are complicated, and specific choices need to be made in order to be precise about either. Nonetheless, generally philosophically speaking: the output of th ...
written 6 weeks ago by seidel6.5k
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Answer: A: RNAseq analysis Deseq
... > I would have expected 200-250 genes in each two grp analysis. Why? What do you know that you aren't describing about your data? I would say that many experiments can give large numbers of DE genes regardless of technique if that is simply the shape of your data. Perhaps you're comparing things ...
written 7 weeks ago by seidel6.5k
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Comment: C: Using R bioconductor for differential gene expression
... If you google the words in the title of your post, you'll find an array of good documentation. Please make some attempt to do some research before asking a question. The result will be better for everyone. Read the Limma Userguide, as mentioned by Fereshteh, it's like a mini-bible on differential g ...
written 7 weeks ago by seidel6.5k
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Comment: C: Bioinformatics to Data Analyst
... Can you elaborate or be more specific with your question? You have a Masters degree in Bioinformatics, and you want to know if it would be good to do data analysis in different parts of the world? Good for what? Good for who? What do you actually want to do? ...
written 7 weeks ago by seidel6.5k
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Comment: C: How to interpret heatmap ?
... There's still something strange about your data, as you describe it: > lcpm<-cpm(y) to find DE genes This is not the command to find DE genes using edgeR. It *is* the command to transform feature counts from integers into counts per million. > what does x-scale -20 to 20 means? the key ...
written 8 weeks ago by seidel6.5k

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