User: Nemo

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Nemo60
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Posts by Nemo

<prev • 31 results • page 1 of 4 • next >
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what is this error for TPP package
... I am trying to install a package from Bioconductor , it gives the following error  Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘VGAM’ Error: package or namespace load failed for ‘TPP’ what does it mean? sessionInfo() R ...
tpp written 5 months ago by Nemo60 • updated 5 months ago by Pariksheet Nanda70
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homologue gene conversion worm to human
... Hello,  I have a large set of worm genes which I would like to homologue to Human or mouse.  Is there a way to do it easily ? the problem is that they are gene names over 8000 Thanks for your comment ...
genetics annotation biomart homologue written 18 months ago by Nemo60
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Comment: C: I get nothing in my up and down regulated genes
... @Laurent Gatto I accepted your answer and I appreciate your help. I found were those zeros are coming from and I solved the issue.  however, I have two questions which are off topic here but seems like you know proteomics and I wanted to ask if you know or not. In a label free quantification. I hav ...
written 18 months ago by Nemo60
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Comment: C: I get nothing in my up and down regulated genes
... @Steve Lianoglou they are LFQ intensities for proteomics. if you look at the column name, you see that I have two control and two treated (which have biological replicate).  why so many zeros ? to be honest i don't know , it is like when you find a protein based on Mass for a sample, an intensity w ...
written 18 months ago by Nemo60
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Comment: C: I get nothing in my up and down regulated genes
... @Laurent Gatto it is right. I guess having the zeros for some proteins comes back to the fact that I analysis few groups of samples together. So, they might have not found for all samples of a group but could have intensities for another group.  I read somewhere that he discarded proteins that had ...
written 18 months ago by Nemo60
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Comment: C: how to find up regulated proteins from a label free
... @Laurent Gatto Thank you so much for your valuable comment. You are right. so I removed those proteins which did not have gene names and also those proteins which their LFQ intensities were zero for all samples control and treated. however, seems like limma does not really get me somewhere too look ...
written 18 months ago by Nemo60
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I get nothing in my up and down regulated genes
... Here is my clean data , I could not post the dput here https://gist.github.com/anonymous/1f8788a5f0f3c40e55995d5c303970c6   Here I try to find up and down regulated genes based on LFQ intensities using limma  design <- model.matrix(~c(rep(1,2),rep(0,2))) fit <- lmFit(data, design) fit2 &l ...
proteomics limma label free written 18 months ago by Nemo60
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Comment: C: how to find up regulated proteins from a label free
... @Laurent Gatto thanks for your message. Is it possible to let me know why? what about other types of proteomics data like SILAC, TMT etc, I guess for them also we cannot use DESeq2, no? is there any paper that used limma for LFQ ?  one technical question, would you remove those genes that have zero ...
written 18 months ago by Nemo60
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how to find up regulated proteins from a label free
... hello,  I have 4 samples two control (one biological replicate) and two treated(one biological replicate). I have obtained the intensities for them called LFQ. Do you think deseq2 is a good way to obtained up regulated proteins ? or should I do it as old school method based on Tueky test etc?  I ...
proteomics deseq2 label free written 18 months ago by Nemo60 • updated 18 months ago by Laurent Gatto900
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Comment: C: getting error with DEseq2
... @James W. MacDonald  of course i do. as I said , if I do make them integer as they are now , i'll lose a lot of info. the best is to normalise them and then use the function "as.integer" in R .  ...
written 21 months ago by Nemo60

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