Mon Sep 17, 2018 3:18 pm by PaulineM
Hi Mike, Zach and Samuel,
Thank you for your answers;
Mike,
I run many tests. At first I noticed that the normalization had an impact on the output in catalyst. But then I run other tests with FCS files which have had exactly the same ‘treatment’ and still the problem persists for some FSC files.
For the last test that I ran:
1. The number of cells did not affect the output
2. I did not have any concatenated files among my files.
3. The conditions were exactly the same for the different files.
4. I did not do any ‘pre-gating’ on these files
5. They were the same sample type (both PBMCs)
On FlowJo I can see that they are events below the 3rd negative decade and above the 13th positive decade (See picture)
Since my first post: I tried to solve the problem by re-writing the FCS files with updatePanel (on R) before running the compensation with CATALYST. It worked for some files, but not all of them.
So I tried re-writing the FCS files with updatePanel (on R) AFTER running the compensation with CATALYST. It worked for all the files I tested so far.
IT SEEMS THE PROBLEM IS SOLVED (I’ll let you know if I encounter another problem)
I am still very curious to know if other users encountered this issue or if I am the only one.
Zach,
Even though, I might have a solution to solve my problem now, I opened an issue in their GitHub repository as you suggested and tagged you
Samuel,
Here are the ouputs for the 2 commands:
> packageVersion("flowCore")
[1] ‘1.46.2’
> con <- file("/Users/maby/Desktop/compensation-test/test compens/original files/withViabLow_1b1.fcs", open="rb")
> dat <- readBin(con = con, what = "raw", n = 8192, size = 1)
> close(con)
> rawToChar(dat)
Error in rawToChar(dat) :
caractère nul au milieu de la chaîne : 'FCS3.0 58 7484 748582727492 0 0|$FIL|withViabLow_1b1.fcs|$TOT|328254|$PAR|63|$BYTEORD|4,3,2,1|$DATATYPE|F|SampleID|1b1|FJ_FCS_VERSION|3|$BEGINANALYSIS|0|$ENDANALYSIS|0|$BEGINSTEXT|0|$ENDSTEXT|0|$NEXTDATA|0|FCSversion|3|CREATOR|PengQiu FCS writer|$COM|PengQiu FCS writer|FILENAME|20171026_IB1_02_1_normalized.fcs|GUID|1.fcs|ORIGINALGUID|1.fcs|$MODE|L|$BTIM|15:58:32|$ETIM|16:20:09|$CYT|DVSSCIENCES-CYTOF-1.0.0|$DATE|26-Oct-2017|$CYTSN|cytof2|$P1S|190BCKG|$P2S|137Ba|$P3S|138Ba|$P4S|209Bi_CD16|$P5S|140Ce_EQBeads1|$P6S|142Ce_CD19|$P7S|133Cs|$P8S|161Dy_CTLA4|$P9S|162Dy_FOXP3|$P10S|163Dy_BTLA|$P11S|164Dy_CD95|$P12S|166Er_CD163|$P13S|167Er_CD27|$P14S|168Er_CD206|$P15S|170Er_CD3|$P16S|151Eu_ICOS|$P17S|153Eu_TIM3|$P19S|155Gd_PD1|$P20S|156Gd_CD49a|$P21S|158Gd_OX40|$P22S|160Gd_CD14|$P23S|165Ho_CD45RO|$P24S|127I|$P25S|115In|$P26S|191Ir_ADN1|$P27S|193Ir_ADN2|$P28S|139La|$P29S|175Lu_PDL1|$P30S|176Lu_CD127|$P31S|143Nd_CD5|$
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