User: Ahdee

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Ahdee40
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40
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New User
Location:
United States
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1 month, 3 weeks ago
Joined:
2 years, 3 months ago
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Posts by Ahdee

<prev • 22 results • page 1 of 3 • next >
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Using tximport to convert a dataframe consisting of tpm to counts for use with limma-voom or edgeR?
... Dear all, I have a dataframe consisting of tpm count generated from another group using RSEM.  However, this only comes with tpm counts only. My goal is to use tximport to convert to this to a count-matrix to use with something like voom-limmar, however the the tutorial I can find so far gives a exa ...
limma rna-seq tximport written 8 weeks ago by Ahdee40 • updated 8 weeks ago by Michael Love15k
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Comment: C: Using of limma moderated t-test with "corrected" expression matrix resulting fr
... Hi Vegard, thanks for the breakdown.  So I'm still a bit confuse on #2.  You mentioned "Batch correction + limma with batch" are you implying to use the corrected matrix but running the model with the batch as a covariate?  So for example,  I have an experiment (Drug vs. control) and did this exper ...
written 12 weeks ago by Ahdee40
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Comment: C: Method for batch correction
... Hi Evan, piggy backing of this thread since I have the same issue.  So I wanted to be clear what you are suggesting.  If I have an experiment (Drug vs. control) and did this experiment on 3 separate cell lines and mainly care about the effect of drug.  Can I run combat to correct for cell line and t ...
written 12 weeks ago by Ahdee40
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Running model separately for each cell line or as the same model?
... Hi, suppose I have an experiment where I compare Drug A to control however I do this experiment with 3 cell lines. Lets say I run an RNA.seq on this and PCA analysis  shows a clear separation of cell lines but within each cell line, Drug and control separates out nicely.  The question is should I ru ...
rnaseq limma edger deseq2 written 12 weeks ago by Ahdee40 • updated 12 weeks ago by k.vitting.seerup20
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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 4 months ago by Ahdee40
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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 5 months ago by Ahdee40
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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 7 months ago by Ahdee40
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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 7 months ago by Ahdee40 • updated 7 months ago by James W. MacDonald45k
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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 10 months ago by Ahdee40
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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 10 months ago by Ahdee40

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