User: Grace_G

gravatar for Grace_G
Grace_G20
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Website:
https://github.com/gmgitx
Last seen:
6 months, 2 weeks ago
Joined:
1 year, 7 months ago
Email:
g******@gmail.com

Posts by Grace_G

<prev • 34 results • page 1 of 4 • next >
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Comment: C: use PCA to see the correlation between samples WT and MT
... Exactly, I forgot to write this step here, so it is `prcomp(t(log2(gene_tpm_matrix+1)), scale=T)` now. Thanks! ...
written 6 months ago by Grace_G20
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use PCA to see the correlation between samples WT and MT
... Hi, Is the code right for to use pca show correlation of samples? **gene_tpm_matrix** rownames are genes, colnames are samples (WT and MT) prcomp(log2(gene_tpm_matrix+1), scale=T) I'm not sure my code(use tpm do log and use scale, I see someone use score), however, so did a test, I use o ...
R next-gen rna-seq written 6 months ago by Grace_G20
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Comment: C: How to quantitative identification outlier from technology replication and biolo
... I see, thanks for sharing these useful ways for thinking and studying, best wishes! ...
written 7 months ago by Grace_G20
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Comment: C: How to quantitative identification outlier from technology replication and biolo
... Thanks a lot! Very helpful and practical idea, I will read these part carefully. And I'm not sure never a good idea mainly means calculate average is will produce decimal point, so can't as input? Actually, why not after process outlier then directly use t-test? since there are many requirements t ...
written 7 months ago by Grace_G20
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How to quantitative identification outlier from technology replication and biological replication
... Hi, **Data:** I get two count matrix (tissue A, tissue B) of genes to identity DEGs, the their includes samples technology replication and biological replication. **To get DEGs:** However, if here no technology replications of each sample, I can directly to do compare. So I'm going to get ave ...
R next-gen rna-seq written 7 months ago by Grace_G20
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Comment: C: RNA-Seq MAplot deviation problem in deseq2
... Thanks! The plot position of right one ![right one][1] like this, "roughly symmetry line" at y=0! [1]: https://gmgitx.github.io/pic/MAplot2.png ...
written 8 months ago by Grace_G20
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RNA-Seq MAplot deviation problem in deseq2
... Here is part(sorry, it's already shows what I want reflect) of my maplot ![my plot][1] [1]: https://gmgitx.github.io/pic/maplot.png The relative distribution of all red point and black point are okay, what is different with normal MAplot is the global plot lower than we expected in general, I m ...
next-gen rna-seq written 8 months ago by Grace_G20
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Comment: C: how to provide background genes to do GO by david
... All of my id likes like, ENSG00000152583 ENSG00000184378 ENSG00000227220 ENSG00000259050 ENSG00000146070 ENSG00000183098 this I opened by sublime text3, if open directly,it looks like ENSG00000152583ENSG00000184378ENSG00000227220ENSG00000259050ENSG00000146070... ...
written 8 months ago by Grace_G20
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Comment: C: how to provide background genes to do GO by david
... Exactly!!! Thanks! Sorry, one more question, if your interested. Still in this process, I ignored these red word "You are either not sure..." in the picture I gave as the following, it's okay in your opinion? ...
written 8 months ago by Grace_G20
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Comment: A: how to provide background genes to do GO by david
... After upload my deg.txt firstly, it ![shows][1] and I choose Option 1 (Recommended) to continue (since my chosen gene id as Ensembl gene id when upload) then, it ![shows][2] actually it can give the GO result, but it without my background gene. I'm not sure here something wrong or not? [1]: ...
written 8 months ago by Grace_G20

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