User: Ahdee

gravatar for Ahdee
Ahdee30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
1 month, 2 weeks ago
Joined:
2 years ago
Email:
s********@gmail.com

Posts by Ahdee

<prev • 18 results • page 1 of 2 • next >
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Why does total unique map not equal to library size?
... Hi I'm using Star align and the build in htseq to count gene features.  however I notice that the final log file, specifically "Uniquely mapped" does not matched the total library size of the count. For example, I could have  sample where the uniquely mapped is 63 million but the the total library ...
rnaseq star htseqcounts written 7 weeks ago by Ahdee30
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Comment: C: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
... @Michael Love , thank you. That was succinct; much appreciate it. Its too bad the toil project in Xena (TCGA) does not provide the library size for this conversion or just the tpm counts.   A ...
written 10 weeks ago by Ahdee30
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Comment: C: LIMMA 2x2 with time
... Thanks James! After reading over you comment I just realized that what I want is indeed the same as the main effect for gene.main.  great thanks again.    ...
written 4 months ago by Ahdee30
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LIMMA 2x2 with time
... Hi can someone take a look at this and see if my design is correct?  What I'm trying to achieve is similar to a 2-way ANOVA main effect and interactions with LIMMA.   I would like to look at the main effect of gene, time and interaction as well as comparison of gene regardless of time. Sorry if thi ...
limma limma design matrix written 4 months ago by Ahdee30 • updated 4 months ago by James W. MacDonald44k
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Comment: C: Minfi error in reading Basename column
... Just to add my 2-bit of info in case someone come across this error.  I kept getting similar error and when I looked I realized that the filenames were incorrectly rendered because originally I used excel to make my sample sheet.  Excel treats the barcode like numbers and thus automatically sets it ...
written 7 months ago by Ahdee30
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RPKM counts with SVA package & Combat with SVA?
... Hi everyone.  2 questions concerning the SVA batch correction package. 1. Can I use RPKM values? Calculated with edgeR rpkm() function with log2 transformed.  I know of svaseq() but that seem to only work with counts.  2. In the manual the author states "It is also possible to use the sva function ...
sva batch effect combat sva written 7 months ago by Ahdee30
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Comment: C: Treating 2 coefficients as the same group in Limma
... cool thanks; also in case someone is reading this for reference, soon after I tested this out by creating a different design with a merge coeffecients: the results were the same.  Aha, yes typo, thanks.    ...
written 12 months ago by Ahdee30
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Treating 2 coefficients as the same group in Limma
... Hi all, I would like to run a GLM using Limma, I have 3 coffecients  biopsy met resect         1       1   0      0   2       1   0      0   3       1   0      0   4       1   0      0  5       1   0      0  6       0   0      1  7       0   0      1   8       0   1      0  9       0   1      0  10 ...
limma glm written 12 months ago by Ahdee30 • updated 12 months ago by James W. MacDonald44k
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Comment: C: Illumina MethylationEPIC vs. 450K
... Would I also be able to use this with other packages like lumi:  for example lumiMethyR requires an annotation IlluminaHumanMethylation450k.db, can I do something like, lumiMethyR("input.txt",lib="IlluminaHumanMethylationEPICanno.ilmn10.hg19") instead? thanks. ...
written 20 months ago by Ahdee30
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Comment: C: Illumina MethylationEPIC vs. 450K
... Peter, this is awesome.  Stupid question but I see two files, one is a manifest file?   Do I just download and install this as usual with install.packages function?   Thanks.  ...
written 20 months ago by Ahdee30

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Popular Question 18 months ago, created a question with more than 1,000 views. For Illumina MethylationEPIC vs. 450K

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