User: jfertaj

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jfertaj20
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New User
Location:
United Kingdom
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1 year, 7 months ago
Joined:
4 years, 2 months ago
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j******@gmail.com

Posts by jfertaj

<prev • 9 results • page 1 of 1 • next >
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Comment: C: missing value in beta matrix after normalization wich champ.norm
... Tnanks @Yuan Tian, I have pasted my code in the question ...
written 19 months ago by jfertaj20
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missing value in beta matrix after normalization wich champ.norm
... Hi , We have a set of 200 samples that we have analysed with EPIC array. I have load the idat.files using champ.load, with autoimpute=T.  The output has no missing values, but when I normalize using champ.norm to run champ.SVD I get missing value again. is that a normal behaviour? should I impute a ...
champ champs.svd() champ.norm written 19 months ago by jfertaj20
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Comment: C: block design to test two factors with limma
... Thanks a lot Aaron for the detailed answer!! ...
written 22 months ago by jfertaj20
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Comment: C: block design to test two factors with limma
... Thanks Aaron Lun, yes I have filtered out low-abundance genes and I have 135 samples, although only 56 controls but I think is enough to get an idea of DEG, and last question, there is no way to test all control vs all disease samples? could I modify somehow design2 to correct for location and test ...
written 22 months ago by jfertaj20
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Comment: C: block design to test two factors with limma
... Post updated @Aaron Lun ...
written 22 months ago by jfertaj20
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block design to test two factors with limma
... Hi, I have posted a similar question few months ago https://support.bioconductor.org/p/94664/, but now I have a doubt if the no differences observed between cases and controls are real or caused by my design or by my misuse of block and duplicateCorrelation  My metadata looks like this one: sa ...
limma voom written 22 months ago by jfertaj20 • updated 22 months ago by Aaron Lun25k
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Comment: C: applying voom + limma to a block factor design in RNA-seq experiment
... Thanks a lot @Aaron, I have corrected the code and also look to the post you mentioned. I was a bit worried because the comparisons Ctrl.distalvsCtrl.proximal,Ctrl.distalvsCtrl.rectum, and Ctrl.proximalvsCtrl.rectum give me a lot of DE genes with really low adjusted pvalue (1x10-e32) and strong B (1 ...
written 2.5 years ago by jfertaj20
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applying voom + limma to a block factor design in RNA-seq experiment
... Hi, I have a block-design for my study where the metadata looks like this: sample_ID location sex polyp_type age status files 1 INTP_103 proximal 1 1 31 ctrl INTP_1031 2 INTP_103 distal 1 1 31 ctrl INTP_1032 3 INTP_103 rectum 1 1 31 c ...
limma voom written 2.5 years ago by jfertaj20
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Find human SNP orthologous flanking sequence
... Hi all,   I would like to ask if it would be possible to retrieve orthologous sequences to a human SNP flanking sequence automatically using biomaRt or another R package. Basically I have a list of 4 human SNPs and I have the flanking sequences (60 kb each side) for each of them. I would like to ...
biomart bioconductor written 4.2 years ago by jfertaj20 • updated 4.2 years ago by Marc Carlson7.2k

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Popular Question 19 months ago, created a question with more than 1,000 views. For applying voom + limma to a block factor design in RNA-seq experiment

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