User: rahel14350

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rahel1435010
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United States
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16 hours ago
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1 year, 8 months ago
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Posts by rahel14350

<prev • 25 results • page 1 of 3 • next >
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Correcting batch effect from known variables in RnBeads using Combat
... Dear all, Can anyone help me on this question on biostar abour RnBeads batch correcting sing ComBat? https://www.biostars.org/p/242980/ many thanks in advance, Rahel   ...
methylation combat batch effect 450k rnbeads written 5 days ago by rahel1435010
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Comment: C: GLM model on time course analysis and removing the outliers in Deseq2
... Many thanks for your explanation. I decided to do factor based analysis and check the output for each time point separately ... ...
written 10 weeks ago by rahel1435010
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Comment: C: GLM model on time course analysis and removing the outliers in Deseq2
... Dear Michael, Many thanks for your time and reply. I understood and I will try to find a statistician around to help me further with a linear design of changes across time. Then, If I want to continue with DeSeq2, I go for Time as a factor and this design: DESeqDataSetFromTximport(txi, colData=co ...
written 10 weeks ago by rahel1435010
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Comment: C: GLM model on time course analysis and removing the outliers in Deseq2
... Dear Gavin,  Many thanks for your reply and explanation. I know if I use time as factor is more flexible but it is not any more linear ...  ...
written 11 weeks ago by rahel1435010
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GLM model on time course analysis and removing the outliers in Deseq2
... Dear Michael, Please accept my apologize in advance for such a lengthy question. I have a data set of 200 RNAseq samples from an experiment on two treatments(trtR/trtNR) and the sampling is done at 7 different time-points. I have different number of replicates: for trtR two replicates and for trtN ...
timecourse deseq2 glm deseq2 independent filtering written 11 weeks ago by rahel1435010 • updated 11 weeks ago by Michael Love11k
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Comment: C: What color is assigned in heatmap for time series analysis
... Many many thanks for your prompt reply, and also for such an amazing program which helped me a lot through my work. I get my answer and I will read your paper before sending the next question ... Cheers, Rahel ...
written 9 months ago by rahel1435010
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Comment: C: What color is assigned in heatmap for time series analysis
... Dear Michael, Many thanks for your reply. I have two treatment response (R, NR) and 7 time points. I want to see DEGs in responses to treatment over time courses. Here is the Deseq2 comment: > ddsTC<-DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=directory, design=~IFX_respons ...
written 9 months ago by rahel1435010
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What color is assigned in heatmap for time series analysis
... Dear all,  can anyone help me with this question which I added in Biostar (https://www.biostars.org/p/197038/) I pasted here to make it easier:  I did DEG analysis for two condition with 5 time points using deseq2. In heatmap I have one colour for each DEG with lowest p- value which represent log ...
deseq2 time course heatmap written 9 months ago by rahel1435010 • updated 9 months ago by EagleEye0
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deseq 2x2: highly variable genes are not among differentially expressed gene
... Hi, I did deseq 2x2 model. When I do a pheatmap for highly variable genes (using rld) the outcome are the genes that they are not even among the differentially expressed genes. Here is my command for pheatmap: topVarGenes <- head(order(rowVars(assay(rld)),decreasing=TRUE),20) mat <- assay(r ...
deseq2 pheatmap rld dds 2x2 model deseq2 written 18 months ago by rahel1435010 • updated 18 months ago by Michael Love11k
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Comment: C: QuasR: Loading BAM files as start point
... Dear Michael, I have a new question. Is that possible to link the "exonjunctions" output to the related gene IDs. I could do this for the exon levels. But is there any way for the Junctions as well? Kind Regards, Rahel ...
written 18 months ago by rahel1435010

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