User: hsharm03@students.poly.edu

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Posts by hsharm03@students.poly.edu

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Answer: A: CummeRbund multiple cases
... Thanks a lot Loyal, I am trying to do a comparison of drug treatment on various resistant and sensitive tumors. I will think about how I can design the cuffdiff analysis to merge them all together. I really appreciate your effort to reply back. Thanks, Himanshu ______________________________________ ...
written 6.4 years ago by hsharm03@students.poly.edu180
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CummeRbund multiple cases
... Dear Community, I have my RNA-seq Differential expression results from Cuffdiff. I would like to make some plots and figures using CummeRbund. I have been using it for quite sometime and find it really good. I wanted to ask if I could combine 2-3 different analyses and merge the results in Cummerbun ...
cummerbund written 6.4 years ago by hsharm03@students.poly.edu180
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Answer: A: Annotation problem through org.Mm.eg.db
... Dear Mailing list, I have mouse gene entrez ids after RNAseq analysis from RSEM and edgeR. I have 13354 gene ids and I am trying to get the gene symbol for the same. I have been doing the following : symbol <- select(org.Mm.eg.db, keys=ids, keytype="ENTREZID", cols="SYMBOL") where ids contains ...
written 6.7 years ago by hsharm03@students.poly.edu180
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Annotation problem through org.Mm.eg.db
... Dear Mailing list, I have mouse gene entrez ids after RNAseq analysis from RSEM and edgeR. I have 13354 gene ids and I am trying to get the gene symbol for the same. I have been doing the following : symbol <- select(org.Mm.eg.db, keys=ids, keytype="ENTREZID", cols="SYMBOL") where ids contains ...
rnaseq written 6.7 years ago by hsharm03@students.poly.edu180 • updated 6.7 years ago by Marc Carlson7.2k
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Removal of duplicate probes
... Dear List, I was wondering if there is a tool which can help me remove the duplicate probes based on the location of the probes?. To be precise, I wanted to select the probe which is closest to the 3'UTR region and discard the others. Is it possible?. Can anyone suggest me what steps to use if a too ...
probe written 6.8 years ago by hsharm03@students.poly.edu180 • updated 6.8 years ago by James W. MacDonald51k
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differential expression analysis for 1 vs 1 experiment
... Dear All, I have data without replicates. So, I have a single file for condition and a single file for control. I know doing a differential analysis will not make any sense statistically. But, I was still interested as a biologist to figure this out. Any suggestion to how I should go ahead with the ...
affy limma written 6.8 years ago by hsharm03@students.poly.edu180 • updated 6.8 years ago by Steve Lianoglou12k
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Comment: C: Filtering out duplicate probes in Affy data
... Thanks a lot James. I really appreciate your help. Also, when I annotate the ids, there should be equal number of probes as after filtering.? How do I lose more when I annotate them?. Thanks, Himanshu From: James W. MacDonald [jmacdon@uw.edu] Sent: Saturday, January 12, 2013 9:48 AM To: Himanshu Sh ...
written 6.9 years ago by hsharm03@students.poly.edu180
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Filtering out duplicate probes in Affy data
... Dear List, I have a set of mouse affy data. They platform is Affy mouse 430a2 chip. There are 8 samples , 4 for each condition. I normalized the data using rma. The array has 22090 probes originally. Then, in order to filter out the genes which have no entrez id, are duplicates for the same gene, I ...
annotation mouse4302 annotate affy written 6.9 years ago by hsharm03@students.poly.edu180 • updated 6.9 years ago by James W. MacDonald51k
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Comment: C: Affy PhenoData
... Dear James, I completely understand the importance of me learning on my own. But, the thing here is this data is not my own experiment. I have been given these 4 files as a test for a job interview. I do not have any other detail regarding it. I just have these 4 cel files. I know the first 3 are w ...
written 7.6 years ago by hsharm03@students.poly.edu180
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Affy PhenoData
... Dear all, I have 4 samples of HT 430mgpm array plate. Three of them are replicates of wild types and 1 is a tumor condition with no replicates. But I do not have any other information regarding how was the experiment conducted and I am not able to figure out how to create a phenodata of the same. W ...
affy limma written 7.6 years ago by hsharm03@students.poly.edu180 • updated 7.6 years ago by James W. MacDonald51k

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Popular Question 6.4 years ago, created a question with more than 1,000 views. For Filtering out duplicate probes in Affy data
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Annotation problem through org.Mm.eg.db

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