User: pbachali

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pbachali10
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Posts by pbachali

<prev • 39 results • page 1 of 4 • next >
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Comment: C: Brainarray CDF with oligopackage
... Thanks a lot. I really appreciate it. I am trying to get the gene symbols, entrezgene for the features from the pd.mogene21st.mm.ense. I am trying to use biomrt but not able to get any results. library(annotate) ID <- featureNames(eset_ba) Symbol <- getSYMBOL(ID,"mogene21stmmentrezg.db") fDat ...
written 14 days ago by pbachali10
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Brainarray CDF with oligopackage
... Hi, I have a dataset from mogene20st platform. I am able to use the oligo package and read the celfiles and get the annotations. I am unable to use the brainarray CDF to read the celfiles. I realized that it's not added in pdInfobuilder. I referred to other posts where the cdf has been Pdinfobuilder ...
oligo brainarray cdf written 14 days ago by pbachali10 • updated 14 days ago by James W. MacDonald50k
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Comment: C: Differential gene expression of time series RNAseq expermimnet with one cohort (
... Thanks for explaining the difference of using LRT and Wald test. Yes I created dds using DESeqDataSetFromMatrix() function and the code for is as follows: dds <- DESeqDataSetFromMatrix(countData = counts.data, colData = metastuff_final, ...
written 29 days ago by pbachali10
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Differential gene expression of time series RNAseq expermimnet with one cohort (diseased)
... Hi, I have a question related to the design of the experiment to perform differential gene expression. I have a RNAseq timeseries experiment of 468 samples at three different time points (T0, week12, week24) of only one cohort (diseased). I don't have two condition here but I have three timepoints o ...
rnaseq timeseries experiment written 29 days ago by pbachali10 • updated 29 days ago by James W. MacDonald50k
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Pipeline for Lexogen Quantseq 3' UTR Sequencing
... I am trying to analyze the RNA Seq samples that were sequenced using Lexogen QuantSeq 3"UTR platform with NextSeq sequences. I was wondering if we could use the same tools we use to analyze the traditional RNA Seq experiment using HiSeq Sequencer. When I say tools, they are FastQC, trimmomatic, STAR ...
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Comment: C: Does GSVA enrichment score comes negative?
... Hi Robert, Firstly my apologies for posting it incorrectly. I thought I would follow the same thread since it is all about GSVA. I would post it correctly next time. Since I have started already here, I am using "ADD REPLY" for now. But from next time I will make sure I am posting the question corr ...
written 14 months ago by pbachali10
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Comment: C: Does GSVA enrichment score comes negative?
... Hi Robert, I have been using GSVA extensively for pathway centric analysis to understand the heterogenous populations and understand the pathways in each patient. This is quite a powerful program. I have a small question. It might be a simple one. As explained in the paper the input for the gsva is ...
written 14 months ago by pbachali10
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Comment: C: annotation for Agilent Mouse an d Human 8x60K array
... Hi All, I am not sure if this is the right place to post this question or not. Since my question is also related to Agilent human microarray annotations, I am trying to follow the same thread. Please feel free to delete the post if this is not relevant here. I am trying to find the annotation packa ...
written 16 months ago by pbachali10
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Comment: C: Differential gene expression of longitudinal data
... Thank you Chris. I would try mixed models with repeated measures. ...
written 18 months ago by pbachali10
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Comment: C: Differential gene expression of longitudinal data
... The patients are paired samples. The patient were enrolled between 2009 to 2011. Basically the patients had follow up visits. For example the patientid 1 is same patient but quantitatively they are different because if you see the age parameter is different. And the reason was not mentioned why few ...
written 18 months ago by pbachali10

Latest awards to pbachali

Popular Question 9 months ago, created a question with more than 1,000 views. For Creating custom geneset
Popular Question 13 months ago, created a question with more than 1,000 views. For Creating custom geneset
Popular Question 23 months ago, created a question with more than 1,000 views. For Creating custom geneset

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